diff --git a/auditbeat/main_test.go b/auditbeat/main_test.go
index f5ad8a4b069e..8b16fe63a583 100644
--- a/auditbeat/main_test.go
+++ b/auditbeat/main_test.go
@@ -35,7 +35,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/filebeat/cmd/generate.go b/filebeat/cmd/generate.go
index 582038716a1e..1e5a4b1a819b 100644
--- a/filebeat/cmd/generate.go
+++ b/filebeat/cmd/generate.go
@@ -26,6 +26,7 @@ import (
 	"github.com/elastic/beats/v7/filebeat/generator/fields"
 	"github.com/elastic/beats/v7/filebeat/generator/fileset"
 	"github.com/elastic/beats/v7/filebeat/generator/module"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/common/cli"
 	"github.com/elastic/elastic-agent-libs/paths"
 )
@@ -63,7 +64,9 @@ func genGenerateModuleCmd() *cobra.Command {
 	}
 
 	genModuleCmd.Flags().String("modules-path", defaultHomePath, "Path to modules directory")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("modules-path")
 	genModuleCmd.Flags().String("es-beats", defaultHomePath, "Path to Elastic Beats")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es-beats")
 
 	return genModuleCmd
 }
@@ -88,7 +91,9 @@ func genGenerateFilesetCmd() *cobra.Command {
 	}
 
 	genFilesetCmd.Flags().String("modules-path", defaultHomePath, "Path to modules directory")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("modules-path")
 	genFilesetCmd.Flags().String("es-beats", defaultHomePath, "Path to Elastic Beats")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es-beats")
 
 	return genFilesetCmd
 }
@@ -113,7 +118,9 @@ func genGenerateFieldsCmd() *cobra.Command {
 	}
 
 	genFieldsCmd.Flags().String("es-beats", defaultHomePath, "Path to Elastic Beats")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es-beats")
 	genFieldsCmd.Flags().Bool("without-documentation", false, "Do not add description fields")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("without-documentation")
 
 	return genFieldsCmd
 }
diff --git a/filebeat/cmd/root.go b/filebeat/cmd/root.go
index 2420a03efdba..48e9c9d74bce 100644
--- a/filebeat/cmd/root.go
+++ b/filebeat/cmd/root.go
@@ -26,6 +26,7 @@ import (
 	"github.com/elastic/beats/v7/filebeat/fileset"
 	"github.com/elastic/beats/v7/filebeat/include"
 	"github.com/elastic/beats/v7/filebeat/input"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 
@@ -49,7 +50,9 @@ func FilebeatSettings(moduleNameSpace string) instance.Settings {
 	}
 	runFlags := pflag.NewFlagSet(Name, pflag.ExitOnError)
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("once"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("once")
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("modules"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("modules")
 	return instance.Settings{
 		RunFlags:      runFlags,
 		Name:          Name,
@@ -66,8 +69,10 @@ func FilebeatSettings(moduleNameSpace string) instance.Settings {
 func Filebeat(inputs beater.PluginFactory, settings instance.Settings) *cmd.BeatsRootCmd {
 	command := cmd.GenRootCmdWithSettings(beater.New(inputs), settings)
 	command.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("M"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("M")
 	command.TestCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("modules"))
 	command.SetupCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("modules"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("modules")
 	command.AddCommand(cmd.GenModulesCmd(Name, "", buildModulesManager))
 	command.AddCommand(genGenerateCmd())
 	return command
diff --git a/filebeat/main_test.go b/filebeat/main_test.go
index ed0486d91cf1..b73c88438e6f 100644
--- a/filebeat/main_test.go
+++ b/filebeat/main_test.go
@@ -41,7 +41,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	fbCommand = fbcmd.Filebeat(inputs.Init, fbcmd.FilebeatSettings(""))
 	fbCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	fbCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/heartbeat/cmd/root.go b/heartbeat/cmd/root.go
index fd95013c6fe0..a1f80a7cda71 100644
--- a/heartbeat/cmd/root.go
+++ b/heartbeat/cmd/root.go
@@ -22,6 +22,7 @@ import (
 
 	"github.com/elastic/beats/v7/heartbeat/beater"
 	"github.com/elastic/beats/v7/heartbeat/include"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	cmd "github.com/elastic/beats/v7/libbeat/cmd"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/ecs"
@@ -81,6 +82,7 @@ func Initialize(settings instance.Settings) *cmd.BeatsRootCmd {
 `
 	setup.ResetFlags()
 	setup.Flags().Bool(cmd.IndexManagementKey, false, "Setup all components related to Elasticsearch index management, including template, ilm policy and rollover alias")
+	cfgfile.AddAllowedBackwardsCompatibleFlag(cmd.IndexManagementKey)
 
 	return rootCmd
 }
diff --git a/heartbeat/main_test.go b/heartbeat/main_test.go
index ac69e001dd3f..18cc332b63af 100644
--- a/heartbeat/main_test.go
+++ b/heartbeat/main_test.go
@@ -34,7 +34,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/libbeat/cfgfile/cfgfile.go b/libbeat/cfgfile/cfgfile.go
index 518d3e3d1550..f19ecad04216 100644
--- a/libbeat/cfgfile/cfgfile.go
+++ b/libbeat/cfgfile/cfgfile.go
@@ -33,14 +33,15 @@ import (
 
 // Evil package level globals
 var (
-	once        sync.Once
-	configfiles *config.StringsFlag
-	overwrites  *config.C
-	defaults    *config.C
-	homePath    *string
-	configPath  *string
-	dataPath    *string
-	logsPath    *string
+	once                            sync.Once
+	configfiles                     *config.StringsFlag
+	overwrites                      *config.C
+	defaults                        *config.C
+	homePath                        *string
+	configPath                      *string
+	dataPath                        *string
+	logsPath                        *string
+	allowedBackwardsCompatibleFlags []string
 )
 
 func Initialize() {
@@ -50,7 +51,9 @@ func Initialize() {
 		// created. See ChangeDefaultCfgfileFlag which should
 		// be called prior to flags.Parse().
 		configfiles = config.StringArrFlag(nil, "c", "beat.yml", "Configuration file, relative to path.config")
+		AddAllowedBackwardsCompatibleFlag("c")
 		overwrites = config.SettingFlag(nil, "E", "Configuration overwrite")
+		AddAllowedBackwardsCompatibleFlag("E")
 		defaults = config.MustNewConfigFrom(map[string]interface{}{
 			"path": map[string]interface{}{
 				"home":   ".", // to be initialized by beat
@@ -60,16 +63,36 @@ func Initialize() {
 			},
 		})
 		homePath = config.ConfigOverwriteFlag(nil, overwrites, "path.home", "path.home", "", "Home path")
+		AddAllowedBackwardsCompatibleFlag("path.home")
 		configPath = config.ConfigOverwriteFlag(nil, overwrites, "path.config", "path.config", "", "Configuration path")
+		AddAllowedBackwardsCompatibleFlag("path.config")
 		dataPath = config.ConfigOverwriteFlag(nil, overwrites, "path.data", "path.data", "", "Data path")
+		AddAllowedBackwardsCompatibleFlag("path.data")
 		logsPath = config.ConfigOverwriteFlag(nil, overwrites, "path.logs", "path.logs", "", "Logs path")
+		AddAllowedBackwardsCompatibleFlag("path.logs")
 	})
 }
 
+func isAllowedBackwardsCompatibleFlag(f string) bool {
+	for _, existing := range allowedBackwardsCompatibleFlags {
+		if existing == f {
+			return true
+		}
+	}
+	return false
+}
+
+func AddAllowedBackwardsCompatibleFlag(f string) {
+	if isAllowedBackwardsCompatibleFlag(f) {
+		return
+	}
+	allowedBackwardsCompatibleFlags = append(allowedBackwardsCompatibleFlags, f)
+}
+
 func ConvertFlagsForBackwardsCompatibility() {
 	// backwards compatibility workaround, convert -flags to --flags:
 	for i, arg := range os.Args[1:] {
-		if strings.HasPrefix(arg, "-") && !strings.HasPrefix(arg, "--") && len(arg) > 2 {
+		if strings.HasPrefix(arg, "-") && !strings.HasPrefix(arg, "--") && isAllowedBackwardsCompatibleFlag(strings.TrimPrefix(arg, "-")) {
 			os.Args[1+i] = "-" + arg
 		}
 	}
diff --git a/libbeat/cmd/export/dashboard.go b/libbeat/cmd/export/dashboard.go
index 7b878e00788b..4a4e13167f8c 100644
--- a/libbeat/cmd/export/dashboard.go
+++ b/libbeat/cmd/export/dashboard.go
@@ -22,6 +22,7 @@ import (
 
 	"github.com/spf13/cobra"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/dashboards"
 	"github.com/elastic/beats/v7/libbeat/version"
@@ -101,8 +102,11 @@ func GenDashboardCmd(settings instance.Settings) *cobra.Command {
 	}
 
 	genTemplateConfigCmd.Flags().String("id", "", "Dashboard id")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("id")
 	genTemplateConfigCmd.Flags().String("yml", "", "Yaml file containing list of dashboard ID and filename pairs")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("yml")
 	genTemplateConfigCmd.Flags().String("folder", "", "Target folder to save exported assets")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("folder")
 
 	return genTemplateConfigCmd
 }
diff --git a/libbeat/cmd/export/ilm_policy.go b/libbeat/cmd/export/ilm_policy.go
index 60c97920fd79..557c62c8aaef 100644
--- a/libbeat/cmd/export/ilm_policy.go
+++ b/libbeat/cmd/export/ilm_policy.go
@@ -20,6 +20,7 @@ package export
 import (
 	"github.com/spf13/cobra"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/idxmgmt"
 	"github.com/elastic/beats/v7/libbeat/idxmgmt/lifecycle"
@@ -57,7 +58,9 @@ func GenGetILMPolicyCmd(settings instance.Settings) *cobra.Command {
 	}
 
 	genTemplateConfigCmd.Flags().String("es.version", settings.Version, "Elasticsearch version")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es.version")
 	genTemplateConfigCmd.Flags().String("dir", "", "Specify directory for printing policy files. By default policies are printed to stdout.")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("dir")
 
 	return genTemplateConfigCmd
 }
diff --git a/libbeat/cmd/export/index_pattern.go b/libbeat/cmd/export/index_pattern.go
index 6b8b8c6839f6..863fc7a72cfe 100644
--- a/libbeat/cmd/export/index_pattern.go
+++ b/libbeat/cmd/export/index_pattern.go
@@ -22,6 +22,7 @@ import (
 
 	"github.com/spf13/cobra"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/kibana"
 	libversion "github.com/elastic/elastic-agent-libs/version"
@@ -67,6 +68,7 @@ func GenIndexPatternConfigCmd(settings instance.Settings) *cobra.Command {
 	}
 
 	genTemplateConfigCmd.Flags().String("es.version", settings.Version, "Elasticsearch version")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es.version")
 
 	return genTemplateConfigCmd
 }
diff --git a/libbeat/cmd/export/template.go b/libbeat/cmd/export/template.go
index ffd957961efe..45a83b986817 100644
--- a/libbeat/cmd/export/template.go
+++ b/libbeat/cmd/export/template.go
@@ -20,6 +20,7 @@ package export
 import (
 	"github.com/spf13/cobra"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/idxmgmt"
 	"github.com/elastic/beats/v7/libbeat/idxmgmt/lifecycle"
@@ -59,8 +60,11 @@ func GenTemplateConfigCmd(settings instance.Settings) *cobra.Command {
 	}
 
 	genTemplateConfigCmd.Flags().String("es.version", settings.Version, "Elasticsearch version")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es.version")
 	genTemplateConfigCmd.Flags().Bool("noilm", false, "Generate template with ILM disabled")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("noilm")
 	genTemplateConfigCmd.Flags().String("dir", "", "Specify directory for printing template files. By default templates are printed to stdout.")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("dir")
 
 	return genTemplateConfigCmd
 }
diff --git a/libbeat/cmd/keystore.go b/libbeat/cmd/keystore.go
index 7f5ecd78c41b..34a1ccc5c220 100644
--- a/libbeat/cmd/keystore.go
+++ b/libbeat/cmd/keystore.go
@@ -29,6 +29,7 @@ import (
 	"github.com/spf13/cobra"
 	tml "golang.org/x/crypto/ssh/terminal"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/common/cli"
 	"github.com/elastic/beats/v7/libbeat/common/terminal"
@@ -74,6 +75,7 @@ func genCreateKeystoreCmd(settings instance.Settings) *cobra.Command {
 		}),
 	}
 	command.Flags().BoolVar(&flagForce, "force", false, "override the existing keystore")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("force")
 	return command
 }
 
@@ -92,7 +94,9 @@ func genAddKeystoreCmd(settings instance.Settings) *cobra.Command {
 		}),
 	}
 	command.Flags().BoolVar(&flagStdin, "stdin", false, "Use the stdin as the source of the secret")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("stdin")
 	command.Flags().BoolVar(&flagForce, "force", false, "Override the existing key")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("force")
 	return command
 }
 
diff --git a/libbeat/cmd/root.go b/libbeat/cmd/root.go
index 8566cced2323..cbe2f7f8f6e5 100644
--- a/libbeat/cmd/root.go
+++ b/libbeat/cmd/root.go
@@ -87,18 +87,30 @@ func GenRootCmdWithSettings(beatCreator beat.Creator, settings instance.Settings
 
 	// Persistent flags, common across all subcommands
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("E"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("E")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("c"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("c")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("d"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("d")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("v"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("v")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("e"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("e")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("environment"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("environment")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("path.config"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("path.config")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("path.data"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("path.data")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("path.logs"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("path.logs")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("path.home"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("path.home")
 	rootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("strict.perms"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("strict.perms")
 	if f := flag.CommandLine.Lookup("plugin"); f != nil {
 		rootCmd.PersistentFlags().AddGoFlag(f)
+		cfgfile.AddAllowedBackwardsCompatibleFlag("plugin")
 	}
 
 	// Inherit root flags from run command
diff --git a/libbeat/cmd/run.go b/libbeat/cmd/run.go
index b078aadaf89c..d6cadd318cee 100644
--- a/libbeat/cmd/run.go
+++ b/libbeat/cmd/run.go
@@ -24,6 +24,7 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/elastic/beats/v7/libbeat/beat"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 )
 
@@ -42,9 +43,13 @@ func genRunCmd(settings instance.Settings, beatCreator beat.Creator) *cobra.Comm
 
 	// Run subcommand flags, only available to *beat run
 	runCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("N"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("N")
 	runCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("httpprof"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("httpprof")
 	runCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("cpuprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("cpuprofile")
 	runCmd.Flags().AddGoFlag(flag.CommandLine.Lookup("memprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("memprofile")
 
 	if settings.RunFlags != nil {
 		runCmd.Flags().AddFlagSet(settings.RunFlags)
diff --git a/libbeat/cmd/setup.go b/libbeat/cmd/setup.go
index 64d1f41fdeaf..0b28d22f96f4 100644
--- a/libbeat/cmd/setup.go
+++ b/libbeat/cmd/setup.go
@@ -24,6 +24,7 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/elastic/beats/v7/libbeat/beat"
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 )
 
@@ -111,11 +112,16 @@ func genSetupCmd(settings instance.Settings, beatCreator beat.Creator) *cobra.Co
 	}
 
 	setup.Flags().Bool(DashboardKey, false, "Setup dashboards")
+	cfgfile.AddAllowedBackwardsCompatibleFlag(DashboardKey)
 	setup.Flags().Bool(PipelineKey, false, "Setup Ingest pipelines")
+	cfgfile.AddAllowedBackwardsCompatibleFlag(PipelineKey)
 	setup.Flags().Bool(IndexManagementKey, false,
 		"Setup all components related to Elasticsearch index management, including template, ilm policy and rollover alias")
+	cfgfile.AddAllowedBackwardsCompatibleFlag(IndexManagementKey)
 	setup.Flags().Bool("enable-all-filesets", false, "Behave as if all modules and filesets had been enabled")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("enable-all-filesets")
 	setup.Flags().Bool("force-enable-module-filesets", false, "Behave as if all filesets, within enabled modules, are enabled")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("force-enable-module-filesets")
 
 	return &setup
 }
diff --git a/libbeat/libbeat_test.go b/libbeat/libbeat_test.go
index 6749376a73a3..1f9e1b3ffe8b 100644
--- a/libbeat/libbeat_test.go
+++ b/libbeat/libbeat_test.go
@@ -32,7 +32,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started
diff --git a/metricbeat/cmd/root.go b/metricbeat/cmd/root.go
index e3d308d2508c..497b71bed8ad 100644
--- a/metricbeat/cmd/root.go
+++ b/metricbeat/cmd/root.go
@@ -24,6 +24,7 @@ import (
 
 	"github.com/elastic/elastic-agent-libs/mapstr"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/ecs"
@@ -61,6 +62,7 @@ func MetricbeatSettings(moduleNameSpace string) instance.Settings {
 	}
 	var runFlags = pflag.NewFlagSet(Name, pflag.ExitOnError)
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("system.hostfs"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("system.hostfs")
 	return instance.Settings{
 		RunFlags:      runFlags,
 		Name:          Name,
diff --git a/metricbeat/main_test.go b/metricbeat/main_test.go
index cd0c73e300ec..495ce5787e04 100644
--- a/metricbeat/main_test.go
+++ b/metricbeat/main_test.go
@@ -34,7 +34,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/packetbeat/cmd/root.go b/packetbeat/cmd/root.go
index 7b1c20b34c6e..eb6d14b1692a 100644
--- a/packetbeat/cmd/root.go
+++ b/packetbeat/cmd/root.go
@@ -22,6 +22,7 @@ import (
 
 	"github.com/spf13/pflag"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	cmd "github.com/elastic/beats/v7/libbeat/cmd"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/libbeat/ecs"
@@ -51,10 +52,15 @@ var RootCmd *cmd.BeatsRootCmd
 func PacketbeatSettings(globals processors.PluginConfig) instance.Settings {
 	runFlags := pflag.NewFlagSet(Name, pflag.ExitOnError)
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("I"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("I")
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("t"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("t")
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("O"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("O")
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("l"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("l")
 	runFlags.AddGoFlag(flag.CommandLine.Lookup("dump"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("dump")
 
 	return instance.Settings{
 		RunFlags:       runFlags,
diff --git a/packetbeat/main_test.go b/packetbeat/main_test.go
index e859028971f2..2dfcfb4572c5 100644
--- a/packetbeat/main_test.go
+++ b/packetbeat/main_test.go
@@ -34,7 +34,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/winlogbeat/main_test.go b/winlogbeat/main_test.go
index d0ffa9518802..002c7431f99a 100644
--- a/winlogbeat/main_test.go
+++ b/winlogbeat/main_test.go
@@ -33,7 +33,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // TestSystem is the function called when the test binary is started.
diff --git a/x-pack/agentbeat/main_test.go b/x-pack/agentbeat/main_test.go
index d3b021283740..b03331b4b52a 100644
--- a/x-pack/agentbeat/main_test.go
+++ b/x-pack/agentbeat/main_test.go
@@ -23,7 +23,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	abCommand = AgentBeat()
 	abCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	abCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/auditbeat/main_test.go b/x-pack/auditbeat/main_test.go
index ecce28993f7c..3456231f5167 100644
--- a/x-pack/auditbeat/main_test.go
+++ b/x-pack/auditbeat/main_test.go
@@ -22,7 +22,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/filebeat/main_test.go b/x-pack/filebeat/main_test.go
index e5a917520fb0..71b32b9e6e86 100644
--- a/x-pack/filebeat/main_test.go
+++ b/x-pack/filebeat/main_test.go
@@ -25,7 +25,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	fbCommand = fbcmd.Filebeat()
 	fbCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	fbCommand.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/functionbeat/main_test.go b/x-pack/functionbeat/main_test.go
index 3191d5265604..1c21f88e2891 100644
--- a/x-pack/functionbeat/main_test.go
+++ b/x-pack/functionbeat/main_test.go
@@ -22,7 +22,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/functionbeat/provider/aws/cmd/root.go b/x-pack/functionbeat/provider/aws/cmd/root.go
index fc7a7e0c2515..c8e7ba17d62b 100644
--- a/x-pack/functionbeat/provider/aws/cmd/root.go
+++ b/x-pack/functionbeat/provider/aws/cmd/root.go
@@ -7,6 +7,7 @@ package cmd
 import (
 	"flag"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/x-pack/functionbeat/function/beater"
 	funcmd "github.com/elastic/beats/v7/x-pack/functionbeat/function/cmd"
 )
@@ -20,6 +21,9 @@ var RootCmd *funcmd.FunctionCmd
 func init() {
 	RootCmd = funcmd.NewFunctionCmd(Name, beater.New)
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("d"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("d")
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("v"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("v")
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("e"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("e")
 }
diff --git a/x-pack/functionbeat/provider/aws/main_test.go b/x-pack/functionbeat/provider/aws/main_test.go
index ea0c47319af6..f180fd28275d 100644
--- a/x-pack/functionbeat/provider/aws/main_test.go
+++ b/x-pack/functionbeat/provider/aws/main_test.go
@@ -21,7 +21,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/functionbeat/provider/local/main_test.go b/x-pack/functionbeat/provider/local/main_test.go
index ec8b5228b19a..7c617b300a65 100644
--- a/x-pack/functionbeat/provider/local/main_test.go
+++ b/x-pack/functionbeat/provider/local/main_test.go
@@ -21,7 +21,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/heartbeat/main_test.go b/x-pack/heartbeat/main_test.go
index b64eb1b33e30..44d5882a9905 100644
--- a/x-pack/heartbeat/main_test.go
+++ b/x-pack/heartbeat/main_test.go
@@ -20,7 +20,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/libbeat/libbeat_test.go b/x-pack/libbeat/libbeat_test.go
index 338ebd7e5fbd..a3df546f3f38 100644
--- a/x-pack/libbeat/libbeat_test.go
+++ b/x-pack/libbeat/libbeat_test.go
@@ -8,6 +8,7 @@ import (
 	"flag"
 	"testing"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/tests/system/template"
 )
 
@@ -18,11 +19,14 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started
 func TestSystem(t *testing.T) {
+	cfgfile.ConvertFlagsForBackwardsCompatibility()
 	if *systemTest {
 		main()
 	}
diff --git a/x-pack/metricbeat/main_test.go b/x-pack/metricbeat/main_test.go
index 7f901cad1aa4..e96a9932765c 100644
--- a/x-pack/metricbeat/main_test.go
+++ b/x-pack/metricbeat/main_test.go
@@ -19,7 +19,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/osquerybeat/main_test.go b/x-pack/osquerybeat/main_test.go
index dc54c98f7e0c..30a9b88efb64 100644
--- a/x-pack/osquerybeat/main_test.go
+++ b/x-pack/osquerybeat/main_test.go
@@ -21,7 +21,9 @@ func init() {
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/packetbeat/main_test.go b/x-pack/packetbeat/main_test.go
index 82f076848475..a332f5c99353 100644
--- a/x-pack/packetbeat/main_test.go
+++ b/x-pack/packetbeat/main_test.go
@@ -19,7 +19,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.
diff --git a/x-pack/winlogbeat/cmd/export.go b/x-pack/winlogbeat/cmd/export.go
index 54f9f02e18c8..facd2fb0e929 100644
--- a/x-pack/winlogbeat/cmd/export.go
+++ b/x-pack/winlogbeat/cmd/export.go
@@ -10,6 +10,7 @@ import (
 
 	"github.com/spf13/cobra"
 
+	"github.com/elastic/beats/v7/libbeat/cfgfile"
 	"github.com/elastic/beats/v7/libbeat/cmd/instance"
 	"github.com/elastic/beats/v7/winlogbeat/module"
 	libversion "github.com/elastic/elastic-agent-libs/version"
@@ -48,7 +49,9 @@ func GenExportPipelineCmd(settings instance.Settings) *cobra.Command {
 	}
 
 	genExportPipelineCmd.Flags().String("es.version", settings.Version, "Elasticsearch version (required)")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("es.version")
 	genExportPipelineCmd.Flags().String("dir", "", "Specify directory for exporting pipelines. Default is current directory.")
+	cfgfile.AddAllowedBackwardsCompatibleFlag("dir")
 
 	return genExportPipelineCmd
 }
diff --git a/x-pack/winlogbeat/main_test.go b/x-pack/winlogbeat/main_test.go
index 1d4fbd8e7a92..b4c0f3b124a1 100644
--- a/x-pack/winlogbeat/main_test.go
+++ b/x-pack/winlogbeat/main_test.go
@@ -19,7 +19,9 @@ func init() {
 	testing.Init()
 	systemTest = flag.Bool("systemTest", false, "Set to true when running system tests")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("systemTest"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("systemTest")
 	cmd.RootCmd.PersistentFlags().AddGoFlag(flag.CommandLine.Lookup("test.coverprofile"))
+	cfgfile.AddAllowedBackwardsCompatibleFlag("test.coverprofile")
 }
 
 // Test started when the test binary is started. Only calls main.