diff --git a/base/database/testing.go b/base/database/testing.go
index 982b73865..ce3e6df6e 100644
--- a/base/database/testing.go
+++ b/base/database/testing.go
@@ -9,7 +9,9 @@ import (
 	"testing"
 	"time"
 
+	"github.com/lib/pq"
 	"github.com/stretchr/testify/assert"
+	"gorm.io/gorm"
 )
 
 func DebugWithCachesCheck(part string, fun func()) {
@@ -173,16 +175,6 @@ func CheckAdvisoriesAccountDataNotified(t *testing.T, rhAccountID int, advisoryI
 	}
 }
 
-func CheckSystemUpdatesCount(t *testing.T, accountID int, systemID int64) []int {
-	var cnt []int
-	assert.NoError(t, Db.Table("system_package spkg").
-		Select("json_array_length(spkg.update_data::json) as len").
-		Where("spkg.update_data is not null").
-		Where("spkg.system_id = ? AND spkg.rh_account_id = ? ", systemID, accountID).
-		Pluck("len", &cnt).Error)
-	return cnt
-}
-
 func CreateReportedAdvisories(reportedAdvisories []string, status []int) map[string]int {
 	reportedAdvisoriesMap := make(map[string]int, len(reportedAdvisories))
 	for i, adv := range reportedAdvisories {
@@ -256,13 +248,27 @@ func CheckEVRAsInDBSynced(t *testing.T, nExpected int, synced bool, evras ...str
 }
 
 func CheckSystemPackages(t *testing.T, accountID int, systemID int64, nExpected int, packageIDs ...int64) {
-	var systemPackages []models.SystemPackage
-	query := Db.Where("rh_account_id = ? AND system_id = ?", accountID, systemID)
+	// check system_package_data
+	var foundIDs []int64
+	sysQuery := Db.Table(`(SELECT jsonb_object_keys(update_data)::bigint as package_id
+							 FROM system_package_data
+							WHERE rh_account_id = ? AND system_id = ?) as t`, accountID, systemID)
+	if len(packageIDs) > 0 {
+		sysQuery = sysQuery.Where("package_id in (?)", packageIDs)
+	}
+	assert.Nil(t, sysQuery.Pluck("package_id", &foundIDs).Error)
+	assert.Equal(t, nExpected, len(foundIDs))
+
+	// check package_system_data
+	var foundNameIDs []int64
+	pkgQuery := Db.Table("package_system_data psd").
+		Where("psd.rh_account_id = ? AND psd.update_data->? IS NOT NULL", accountID, strconv.FormatInt(systemID, 10))
 	if len(packageIDs) > 0 {
-		query = query.Where("package_id IN (?)", packageIDs)
+		pkgQuery = pkgQuery.Joins("JOIN package p ON p.name_id = psd.package_name_id").
+			Where("p.id in (?)", packageIDs)
 	}
-	assert.Nil(t, query.Find(&systemPackages).Error)
-	assert.Equal(t, nExpected, len(systemPackages))
+	assert.Nil(t, pkgQuery.Pluck("package_name_id", &foundNameIDs).Error)
+	assert.Equal(t, nExpected, len(foundNameIDs))
 }
 
 func CheckSystemRepos(t *testing.T, rhAccountID int, systemID int64, repoIDs []int64) {
@@ -296,15 +302,34 @@ func DeleteAdvisoryAccountData(t *testing.T, rhAccountID int, advisoryIDs []int6
 }
 
 func DeleteSystemPackages(t *testing.T, accountID int, systemID int64, pkgIDs ...int64) {
-	query := Db.Model(&models.SystemPackage{}).Where("rh_account_id = ? AND system_id = ?", accountID, systemID)
+	// delete system_package_data
 	if len(pkgIDs) > 0 {
-		query = query.Where("package_id in (?)", pkgIDs)
+		keys := make([]string, len(pkgIDs))
+		for i, pid := range pkgIDs {
+			keys[i] = strconv.FormatInt(pid, 10)
+		}
+		assert.Nil(t, Db.Model(&models.SystemPackageData{}).
+			Where("rh_account_id = ? and system_id = ?", accountID, systemID).
+			Update("update_data", gorm.Expr("update_data - ?", pq.StringArray(keys))).Error)
+	} else {
+		assert.Nil(t, Db.Where("rh_account_id = ? AND system_id = ?", accountID, systemID).
+			Delete(&models.SystemPackageData{}).Error)
 	}
-	assert.Nil(t, query.Delete(&models.SystemPackage{}).Error)
 
-	var count int64 // ensure deleted
-	assert.Nil(t, query.Count(&count).Error)
-	assert.Equal(t, int64(0), count)
+	// delete package_system_data
+	systemIDKey := strconv.FormatInt(systemID, 10)
+	if len(pkgIDs) > 0 {
+		assert.Nil(t, Db.Exec(`UPDATE package_system_data psd SET update_data = update_data - ?
+						   FROM package p
+						  WHERE psd.rh_account_id = ?
+						    AND psd.update_data->? IS NOT NULL
+						    AND p.name_id = psd.package_name_id
+						    AND p.id in (?)`, systemIDKey, accountID, systemIDKey, pkgIDs).Error)
+	} else {
+		query := Db.Table("package_system_data psd").
+			Where("psd.rh_account_id = ? AND psd.update_data->? IS NOT NULL", accountID, systemIDKey)
+		assert.Nil(t, query.Update("update_data", gorm.Expr("update_data - ?", strconv.FormatInt(systemID, 10))).Error)
+	}
 }
 
 func DeleteSystemRepos(t *testing.T, rhAccountID int, systemID int64, repoIDs []int64) {
diff --git a/evaluator/evaluate_test.go b/evaluator/evaluate_test.go
index 711c160eb..9a341974c 100644
--- a/evaluator/evaluate_test.go
+++ b/evaluator/evaluate_test.go
@@ -135,14 +135,6 @@ func TestEvaluateYum(t *testing.T) {
 	assert.Equal(t, 1, len(mockWriter.Messages))
 }
 
-func TestEvaluatePruneUpdates(t *testing.T) {
-	TestEvaluate(t)
-	count := database.CheckSystemUpdatesCount(t, rhAccountID, systemID)
-	for _, c := range count {
-		assert.LessOrEqual(t, c, 1, "All packages should only have single update stored")
-	}
-}
-
 func TestRun(t *testing.T) {
 	configure()
 	var nReaders int32