diff --git a/pkg/provisioning/service.go b/pkg/provisioning/service.go
index f305ff104..c49260135 100644
--- a/pkg/provisioning/service.go
+++ b/pkg/provisioning/service.go
@@ -102,6 +102,23 @@ func (s *Service) Init(ctx context.Context) error {
 		allPls = append(allPls, duplicateID)
 	}
 
+	// remove pipelines with duplicate IDs from API pipelines
+	var apiProvisioned []int
+	for i, pl := range configs {
+		pipelineInstance, err := s.pipelineService.Get(ctx, pl.ID)
+		if err != nil {
+			if !cerrors.Is(err, pipeline.ErrInstanceNotFound) {
+				multierr = multierror.Append(multierr, cerrors.Errorf("error getting pipeline instance with ID %q: %w", pl.ID, err))
+			}
+			continue
+		}
+		if pipelineInstance.ProvisionedBy != pipeline.ProvisionTypeConfig {
+			multierr = multierror.Append(multierr, cerrors.Errorf("pipelines with ID %q will be skipped: %w", pl.ID, ErrNotProvisionedByConfig))
+			apiProvisioned = append(apiProvisioned, i)
+		}
+	}
+	configs = s.deleteIndexes(configs, apiProvisioned)
+
 	// contains pipelineIDs of successfully provisioned pipelines.
 	var successPls []string
 	for _, cfg := range configs {
diff --git a/pkg/provisioning/service_test.go b/pkg/provisioning/service_test.go
index 5112c921e..f036b9709 100644
--- a/pkg/provisioning/service_test.go
+++ b/pkg/provisioning/service_test.go
@@ -110,10 +110,12 @@ func TestService_Init_Create(t *testing.T) {
 	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines1"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	// pipeline doesn't exist
 	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
-
 	// create pipeline
 	pipelineService.EXPECT().CreateWithInstance(anyCtx, p1.P1)
 	pipelineService.EXPECT().UpdateDLQ(anyCtx, p1.P1.ID, p1.P1.DLQ)
@@ -144,6 +146,9 @@ func TestService_Init_Update(t *testing.T) {
 	service.pipelinesPath = "./test/pipelines1"
 
 	pipelineService.EXPECT().List(anyCtx)
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	// pipeline exists
 	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(oldPipelineInstance, nil)
 
@@ -204,6 +209,9 @@ func TestService_Init_NoRollbackOnFailedStart(t *testing.T) {
 	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines1"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
 
@@ -237,6 +245,9 @@ func TestService_Init_RollbackCreate(t *testing.T) {
 	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines1"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
 
@@ -273,6 +284,9 @@ func TestService_Init_RollbackUpdate(t *testing.T) {
 	service, pipelineService, connService, procService, _ := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines1"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	// pipeline exists
 	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(oldPipelineInstance, nil)
@@ -310,6 +324,9 @@ func TestService_Init_MultiplePipelinesDuplicatedPipelineID(t *testing.T) {
 	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines2"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p2.P2.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	pipelineService.EXPECT().Get(anyCtx, p2.P2.ID).Return(nil, pipeline.ErrInstanceNotFound)
 
@@ -336,6 +353,10 @@ func TestService_Init_MultiplePipelines(t *testing.T) {
 	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
 	service.pipelinesPath = "./test/pipelines3"
 
+	// return a pipeline not provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p3.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+	pipelineService.EXPECT().Get(anyCtx, p3.P2.ID).Return(nil, pipeline.ErrInstanceNotFound)
+
 	pipelineService.EXPECT().List(anyCtx)
 	pipelineService.EXPECT().Get(anyCtx, p3.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
 	pipelineService.EXPECT().Get(anyCtx, p3.P2.ID).Return(nil, pipeline.ErrInstanceNotFound)
@@ -366,6 +387,63 @@ func TestService_Init_MultiplePipelines(t *testing.T) {
 	is.NoErr(err)
 }
 
+func TestService_Init_PipelineProvisionedFromAPI(t *testing.T) {
+	is := is.New(t)
+	logger := log.Nop()
+	ctrl := gomock.NewController(t)
+
+	tmp := *oldPipelineInstance
+	APIPipelineInstance := &tmp
+	APIPipelineInstance.ProvisionedBy = pipeline.ProvisionTypeAPI // change the test pipeline to be API provisioned
+
+	service, pipelineService, _, _, _ := newTestService(ctrl, logger)
+	service.pipelinesPath = "./test/pipelines1"
+
+	// pipeline provisioned by API
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(APIPipelineInstance, nil)
+
+	pipelineService.EXPECT().List(anyCtx)
+
+	err := service.Init(context.Background())
+	is.True(cerrors.Is(err, ErrNotProvisionedByConfig))
+}
+
+func TestService_Init_PipelineProvisionedFromAPI_Error(t *testing.T) {
+	is := is.New(t)
+	logger := log.Nop()
+	ctrl := gomock.NewController(t)
+	otherErr := cerrors.New("GetError")
+
+	service, pipelineService, connService, procService, plugService := newTestService(ctrl, logger)
+	service.pipelinesPath = "./test/pipelines1"
+
+	// error from calling Get
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, otherErr)
+
+	pipelineService.EXPECT().List(anyCtx)
+	// pipeline doesn't exist
+	pipelineService.EXPECT().Get(anyCtx, p1.P1.ID).Return(nil, pipeline.ErrInstanceNotFound)
+	// create pipeline
+	pipelineService.EXPECT().CreateWithInstance(anyCtx, p1.P1)
+	pipelineService.EXPECT().UpdateDLQ(anyCtx, p1.P1.ID, p1.P1.DLQ)
+	pipelineService.EXPECT().AddConnector(anyCtx, p1.P1.ID, p1.P1.ConnectorIDs[0])
+	pipelineService.EXPECT().AddConnector(anyCtx, p1.P1.ID, p1.P1.ConnectorIDs[1])
+	pipelineService.EXPECT().AddProcessor(anyCtx, p1.P1.ID, p1.P1.ProcessorIDs[0])
+
+	connService.EXPECT().CreateWithInstance(anyCtx, p1.P1C1)
+	connService.EXPECT().CreateWithInstance(anyCtx, p1.P1C2)
+	connService.EXPECT().AddProcessor(anyCtx, p1.P1C2.ID, p1.P1C2.ProcessorIDs[0])
+
+	procService.EXPECT().CreateWithInstance(anyCtx, p1.P1C2P1)
+	procService.EXPECT().CreateWithInstance(anyCtx, p1.P1P1)
+
+	// start pipeline
+	pipelineService.EXPECT().Start(anyCtx, connService, procService, plugService, p1.P1.ID)
+
+	err := service.Init(context.Background())
+	is.True(cerrors.Is(err, otherErr))
+}
+
 func TestService_Delete(t *testing.T) {
 	is := is.New(t)
 	logger := log.Nop()
@@ -379,7 +457,6 @@ func TestService_Delete(t *testing.T) {
 	connService.EXPECT().Get(anyCtx, oldConnector2Instance.ID).Return(oldConnector2Instance, nil)
 	procService.EXPECT().Get(anyCtx, oldConnectorProcessorInstance.ID).Return(oldConnectorProcessorInstance, nil)
 	procService.EXPECT().Get(anyCtx, oldPipelineProcessorInstance.ID).Return(oldPipelineProcessorInstance, nil)
-
 	// delete pipeline
 	pipelineService.EXPECT().Delete(anyCtx, oldPipelineInstance.ID).Return(nil)
 	connService.EXPECT().Delete(anyCtx, oldConnector1Instance.ID, plugService).Return(nil)