diff --git a/session/sql_migration.go b/session/sql_migration.go
index 5e280d50c..a2498beda 100644
--- a/session/sql_migration.go
+++ b/session/sql_migration.go
@@ -198,6 +198,7 @@ func migrateSessionsToSQLAndValidate(ctx context.Context,
 		overrideSessionTimeZone(migratedSession)
 		overrideMacaroonRecipe(kvSession, migratedSession)
 		overrideRemovedAccount(kvSession, migratedSession)
+		overrideFeatureConfig(kvSession, migratedSession)
 
 		if !reflect.DeepEqual(kvSession, migratedSession) {
 			diff := difflib.UnifiedDiff{
@@ -530,3 +531,28 @@ func overrideRemovedAccount(kvSession *Session, migratedSession *Session) {
 		},
 	)
 }
+
+// overrideFeatureConfig overrides a specific feature's config for the SQL
+// session in a certain scenario:
+//
+// In the bbolt store, an empty config for a feature is represented as an empty
+// array, while in for the SQL store, the same config is represented as nil.
+// Therefore, in the scenario where a specific feature has an empty config, we
+// override the SQL FeatureConfig for that feature to also be set to an empty
+// array. This is needed to ensure that the deep equals check in the migration
+// validation does not fail in this scenario.
+func overrideFeatureConfig(kvSession *Session, mSession *Session) {
+	// If FeatureConfig is not set for both sessions, we return early.
+	if kvSession.FeatureConfig == nil || mSession.FeatureConfig == nil {
+		return
+	}
+
+	migratedConf := *mSession.FeatureConfig
+	for featureName, config := range *kvSession.FeatureConfig {
+		// If the config is empty for the feature, we override
+		// the SQL version.
+		if len(config) == 0 {
+			migratedConf[featureName] = make([]byte, 0)
+		}
+	}
+}
diff --git a/session/sql_migration_test.go b/session/sql_migration_test.go
index 1cb7ba751..fb8763808 100644
--- a/session/sql_migration_test.go
+++ b/session/sql_migration_test.go
@@ -81,6 +81,10 @@ func TestSessionsStoreMigration(t *testing.T) {
 			// session doesn't.
 			overrideRemovedAccount(kvSession, sqlSession)
 
+			// Finally, we also need to override specific feature's
+			// config if they are empty.
+			overrideFeatureConfig(kvSession, sqlSession)
+
 			assertEqualSessions(t, kvSession, sqlSession)
 		}
 
@@ -200,6 +204,48 @@ func TestSessionsStoreMigration(t *testing.T) {
 				return getBoltStoreSessions(t, store)
 			},
 		},
+		{
+			name: "one session with a feature config with empty",
+			populateDB: func(t *testing.T, store *BoltStore,
+				_ accounts.Store) []*Session {
+
+				// Set a feature config, which has an empty
+				// entry for a specific feature.
+				featureConfig := map[string][]byte{
+					"AutoFees": {},
+				}
+
+				_, err := store.NewSession(
+					ctx, "test", TypeMacaroonAdmin,
+					time.Unix(1000, 0), "",
+					WithFeatureConfig(featureConfig),
+				)
+				require.NoError(t, err)
+
+				return getBoltStoreSessions(t, store)
+			},
+		},
+		{
+			name: "one session with a feature config with nil",
+			populateDB: func(t *testing.T, store *BoltStore,
+				_ accounts.Store) []*Session {
+
+				// Set a feature config, which has a nil entry
+				// for a specific feature.
+				featureConfig := map[string][]byte{
+					"AutoFees": nil,
+				}
+
+				_, err := store.NewSession(
+					ctx, "test", TypeMacaroonAdmin,
+					time.Unix(1000, 0), "",
+					WithFeatureConfig(featureConfig),
+				)
+				require.NoError(t, err)
+
+				return getBoltStoreSessions(t, store)
+			},
+		},
 		{
 			name: "one session with dev server",
 			populateDB: func(t *testing.T, store *BoltStore,
@@ -801,9 +847,18 @@ func randomPrivacyFlags() PrivacyFlags {
 func randomFeatureConfig() FeaturesConfig {
 	featureConfig := make(FeaturesConfig)
 	for i := range rand.Intn(10) {
-		featureName := fmt.Sprintf("feature%d", i)
-		featureValue := []byte{byte(rand.Int31())}
-		featureConfig[featureName] = featureValue
+		var (
+			featureName = fmt.Sprintf("feature%d", i)
+			configValue []byte
+		)
+
+		// For the vast majority of the features, we set a value for the
+		// feature's config. But in 1/5 of the cases, we set an empty
+		// config.
+		if rand.Intn(5) != 0 {
+			configValue = []byte{byte(rand.Int31())}
+		}
+		featureConfig[featureName] = configValue
 	}
 
 	return featureConfig