diff --git a/pkg/services/provisioning/datasources/config_reader.go b/pkg/services/provisioning/datasources/config_reader.go
index d7f37602d30..243c2f726ab 100644
--- a/pkg/services/provisioning/datasources/config_reader.go
+++ b/pkg/services/provisioning/datasources/config_reader.go
@@ -93,11 +93,11 @@ func (cr *configReader) parseDatasourceConfig(path string, file os.FileInfo) (*c
 func (cr *configReader) validateDefaultUniqueness(ctx context.Context, datasources []*configs) error {
 	defaultCount := map[int64]int{}
 	for i := range datasources {
-		if datasources[i].Datasources == nil {
-			continue
-		}
-
 		for _, ds := range datasources[i].Datasources {
+			if ds == nil {
+				continue
+			}
+
 			if ds.OrgID == 0 {
 				ds.OrgID = 1
 			}
@@ -115,6 +115,10 @@ func (cr *configReader) validateDefaultUniqueness(ctx context.Context, datasourc
 		}
 
 		for _, ds := range datasources[i].DeleteDatasources {
+			if ds == nil {
+				continue
+			}
+
 			if ds.OrgID == 0 {
 				ds.OrgID = 1
 			}
diff --git a/pkg/services/provisioning/datasources/config_reader_test.go b/pkg/services/provisioning/datasources/config_reader_test.go
index 8db0f53dc0a..769440e25f9 100644
--- a/pkg/services/provisioning/datasources/config_reader_test.go
+++ b/pkg/services/provisioning/datasources/config_reader_test.go
@@ -18,6 +18,7 @@ var (
 
 	twoDatasourcesConfig            = "testdata/two-datasources"
 	twoDatasourcesConfigPurgeOthers = "testdata/insert-two-delete-two"
+	deleteOneDatasource             = "testdata/delete-one"
 	doubleDatasourcesConfig         = "testdata/double-default"
 	allProperties                   = "testdata/all-properties"
 	versionZero                     = "testdata/version-0"
@@ -129,6 +130,27 @@ func TestDatasourceAsConfig(t *testing.T) {
 		})
 	})
 
+	t.Run("Remove one datasource", func(t *testing.T) {
+		setup()
+		t.Run("Remove one datasource", func(t *testing.T) {
+			fakeRepo.loadAll = []*models.DataSource{}
+
+			t.Run("should have removed old datasource", func(t *testing.T) {
+				dc := newDatasourceProvisioner(logger)
+				err := dc.applyChanges(context.Background(), deleteOneDatasource)
+				if err != nil {
+					t.Fatalf("applyChanges return an error %v", err)
+				}
+
+				require.Equal(t, 1, len(fakeRepo.deleted))
+				// should have set OrgID to 1
+				require.Equal(t, fakeRepo.deleted[0].OrgID, int64(1))
+				require.Equal(t, 0, len(fakeRepo.inserted))
+				require.Equal(t, len(fakeRepo.updated), 0)
+			})
+		})
+	})
+
 	t.Run("Two configured datasource and purge others ", func(t *testing.T) {
 		setup()
 		t.Run("two other datasources in database", func(t *testing.T) {
diff --git a/pkg/services/provisioning/datasources/testdata/delete-one/one-datasource.yaml b/pkg/services/provisioning/datasources/testdata/delete-one/one-datasource.yaml
new file mode 100644
index 00000000000..3ffb62d4e6c
--- /dev/null
+++ b/pkg/services/provisioning/datasources/testdata/delete-one/one-datasource.yaml
@@ -0,0 +1,3 @@
+datasources: []
+delete_datasources:
+  - name: old-data-source