diff --git a/command-snapshot.json b/command-snapshot.json
index 69009d712..3f8979637 100644
--- a/command-snapshot.json
+++ b/command-snapshot.json
@@ -239,6 +239,7 @@
     "flagChars": ["c", "d", "m", "n", "p", "t"],
     "flags": [
       "api-version",
+      "exclude-metadata",
       "flags-dir",
       "from-org",
       "include-packages",
diff --git a/messages/manifest.generate.md b/messages/manifest.generate.md
index be2d55498..5fcd969cf 100644
--- a/messages/manifest.generate.md
+++ b/messages/manifest.generate.md
@@ -19,6 +19,8 @@ Use --name to specify a custom name for the generated manifest if the pre-define
 
 To include multiple metadata components, either set multiple --metadata <name> flags or a single --metadata flag with multiple names separated by spaces. Enclose names that contain spaces in one set of double quotes. The same syntax applies to --include-packages and --source-dir.
 
+To build a manifest from the metadata in an org use the --from-org flag optionally combining it with the --metadata flag to only include certain metadata types, or the --exclude-metadata flag to exclude certain metadata types. When building a manifest from an org, the command makes many API calls concurrently to discover the metadata that exists in the org. To limit the number of concurrent requests use the `SF_LIST_METADATA_BATCH_SIZE` environment variable and set it to a size that works best for your org and environment. If you are experiencing timeouts and/or inconsistent manifest contents then setting this environment variable should improve accuracy. However, the command will take longer to run since it sends fewer requests at a time.
+
 # examples
 
 - Create a manifest for deploying or retrieving all Apex classes and custom objects:
@@ -37,10 +39,22 @@ To include multiple metadata components, either set multiple --metadata <name> f
 
   $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --include-packages unlocked
 
+- Create a manifest from specific metadata types in an org:
+
+  $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --metadata ApexClass,CustomObject,CustomLabels
+
+- Create a manifest from all metadata components in an org excluding specific metadata types:
+
+  $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --exclude-metadata StandardValueSet
+
 # flags.include-packages.summary
 
 Package types (managed, unlocked) whose metadata is included in the manifest; by default, metadata in managed and unlocked packages is excluded. Metadata in unmanaged packages is always included.
 
+# flags.exclude-metadata.summary
+
+Metadata types (types only; not names) to exclude when building a manifest from an org.
+
 # flags.from-org.summary
 
 Username or alias of the org that contains the metadata components from which to build a manifest.
diff --git a/package.json b/package.json
index 4f39be226..7f00484d9 100644
--- a/package.json
+++ b/package.json
@@ -12,7 +12,7 @@
     "@salesforce/kit": "^3.2.3",
     "@salesforce/plugin-info": "^3.4.23",
     "@salesforce/sf-plugins-core": "^12.0.11",
-    "@salesforce/source-deploy-retrieve": "^12.10.2",
+    "@salesforce/source-deploy-retrieve": "12.10.4-dev-17431548.0",
     "@salesforce/source-tracking": "^7.1.17",
     "@salesforce/ts-types": "^2.0.12",
     "ansis": "^3.3.2",
diff --git a/src/commands/project/generate/manifest.ts b/src/commands/project/generate/manifest.ts
index 3d04f9d37..a38c9979f 100644
--- a/src/commands/project/generate/manifest.ts
+++ b/src/commands/project/generate/manifest.ts
@@ -38,7 +38,7 @@ export type ManifestGenerateCommandResult = {
   path: string;
 };
 
-const xorFlags = ['metadata', 'source-dir', 'from-org'];
+const atLeastOneOfFlags = ['metadata', 'source-dir', 'from-org'];
 
 export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
   public static readonly summary = messages.getMessage('summary');
@@ -53,14 +53,14 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
     metadata: arrayWithDeprecation({
       char: 'm',
       summary: messages.getMessage('flags.metadata.summary'),
-      exactlyOne: xorFlags,
+      exclusive: ['source-dir'],
     }),
     'source-dir': arrayWithDeprecation({
       char: 'p',
       aliases: ['sourcepath'],
       deprecateAliases: true,
       summary: messages.getMessage('flags.source-dir.summary'),
-      exactlyOne: xorFlags,
+      exclusive: ['metadata'],
     }),
     name: Flags.string({
       char: 'n',
@@ -85,11 +85,18 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
       char: 'c',
       dependsOn: ['from-org'],
     }),
+    'exclude-metadata': Flags.string({
+      multiple: true,
+      delimiter: ',',
+      summary: messages.getMessage('flags.exclude-metadata.summary'),
+      dependsOn: ['from-org'],
+      exclusive: ['metadata'],
+    }),
     'from-org': Flags.custom({
       summary: messages.getMessage('flags.from-org.summary'),
-      exactlyOne: xorFlags,
       aliases: ['fromorg'],
       deprecateAliases: true,
+      exclusive: ['source-dir'],
       parse: async (input: string | undefined) => (input ? Org.create({ aliasOrUsername: input }) : undefined),
     })(),
     'output-dir': Flags.string({
@@ -102,6 +109,12 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
 
   public async run(): Promise<ManifestGenerateCommandResult> {
     const { flags } = await this.parse(ManifestGenerate);
+
+    // We need at least one of these flags (but could be more than 1): 'metadata', 'source-dir', 'from-org'
+    if (!Object.keys(flags).some((f) => atLeastOneOfFlags.includes(f))) {
+      throw Error(`provided flags must include at least one of: ${atLeastOneOfFlags.toString()}`);
+    }
+
     // convert the manifesttype into one of the "official" manifest names
     // if no manifesttype flag passed, use the manifestname?flag
     // if no manifestname flag, default to 'package.xml'
@@ -114,12 +127,14 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
     const componentSet = await ComponentSetBuilder.build({
       apiversion: flags['api-version'] ?? (await getSourceApiVersion()),
       sourcepath: flags['source-dir'],
-      metadata: flags.metadata
-        ? {
-            metadataEntries: flags.metadata,
-            directoryPaths: await getPackageDirs(),
-          }
-        : undefined,
+      metadata:
+        flags.metadata ?? flags['exclude-metadata']
+          ? {
+              metadataEntries: flags.metadata ?? [],
+              directoryPaths: await getPackageDirs(),
+              excludedEntries: flags['exclude-metadata'],
+            }
+          : undefined,
       org: flags['from-org']
         ? {
             username: flags['from-org'].getUsername() as string,
diff --git a/test/tsconfig.json b/test/tsconfig.json
index a5f451cf0..b62002f08 100644
--- a/test/tsconfig.json
+++ b/test/tsconfig.json
@@ -2,6 +2,10 @@
   "extends": "@salesforce/dev-config/tsconfig-test-strict-esm",
   "include": ["./**/*.ts"],
   "compilerOptions": {
-    "skipLibCheck": true
+    "skipLibCheck": true,
+    "baseUrl": "..",
+    "paths": {
+      "@salesforce/source-deploy-retrieve": ["node_modules/@salesforce/source-deploy-retrieve"]
+    }
   }
 }
diff --git a/tsconfig.json b/tsconfig.json
index 1fa9d6311..5dbc2628b 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -4,7 +4,10 @@
     "outDir": "lib",
     "rootDir": "src",
     "skipLibCheck": true,
-    "baseUrl": "."
+    "baseUrl": ".",
+    "paths": {
+      "@salesforce/source-deploy-retrieve": ["node_modules/@salesforce/source-deploy-retrieve"]
+    }
   },
   "include": ["./src/**/*.ts"]
 }
diff --git a/yarn.lock b/yarn.lock
index 297108949..7e031d39c 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1671,6 +1671,25 @@
     cli-progress "^3.12.0"
     terminal-link "^3.0.0"
 
+"@salesforce/source-deploy-retrieve@12.10.4-dev-17431548.0":
+  version "12.10.4-dev-17431548.0"
+  resolved "https://registry.yarnpkg.com/@salesforce/source-deploy-retrieve/-/source-deploy-retrieve-12.10.4-dev-17431548.0.tgz#3d1214fa7b69c9e4eaf68912cad198d55208b15c"
+  integrity sha512-tAvqDNp3Oa0QDGhs1rJCOJQYvRO7pfKxzWutjVN2g7fbxn/ej5U5ZX6hKfCp411+NmI7MsN5wUpjQOs185h0mA==
+  dependencies:
+    "@salesforce/core" "^8.8.0"
+    "@salesforce/kit" "^3.2.2"
+    "@salesforce/ts-types" "^2.0.12"
+    fast-levenshtein "^3.0.0"
+    fast-xml-parser "^4.5.0"
+    got "^11.8.6"
+    graceful-fs "^4.2.11"
+    ignore "^5.3.2"
+    isbinaryfile "^5.0.2"
+    jszip "^3.10.1"
+    mime "2.6.0"
+    minimatch "^9.0.5"
+    proxy-agent "^6.4.0"
+
 "@salesforce/source-deploy-retrieve@^12.10.2", "@salesforce/source-deploy-retrieve@^12.7.4":
   version "12.10.2"
   resolved "https://registry.yarnpkg.com/@salesforce/source-deploy-retrieve/-/source-deploy-retrieve-12.10.2.tgz#c3737f3751f84cb4754b666edd83c014c91b87bb"