diff --git a/web/app/components/app/configuration/dataset-config/index.tsx b/web/app/components/app/configuration/dataset-config/index.tsx
index dfa243b8aa..f960ea7edb 100644
--- a/web/app/components/app/configuration/dataset-config/index.tsx
+++ b/web/app/components/app/configuration/dataset-config/index.tsx
@@ -256,6 +256,7 @@ const DatasetConfig: FC = () => {
       <div className='py-2 border-t border-t-divider-subtle'>
         <MetadataFilter
           metadataList={metadataList}
+          selectedDatasetsLoaded
           metadataFilterMode={datasetConfigs.metadata_filtering_mode}
           metadataFilteringConditions={datasetConfigs.metadata_filtering_conditions}
           handleAddCondition={handleAddCondition}
diff --git a/web/app/components/workflow/nodes/knowledge-retrieval/components/metadata/metadata-trigger.tsx b/web/app/components/workflow/nodes/knowledge-retrieval/components/metadata/metadata-trigger.tsx
index 6ed77b4dc8..cfb96fa293 100644
--- a/web/app/components/workflow/nodes/knowledge-retrieval/components/metadata/metadata-trigger.tsx
+++ b/web/app/components/workflow/nodes/knowledge-retrieval/components/metadata/metadata-trigger.tsx
@@ -2,6 +2,7 @@ import {
   useEffect,
   useState,
 } from 'react'
+import { unionBy } from 'lodash-es'
 import { useTranslation } from 'react-i18next'
 import { RiFilter3Line } from '@remixicon/react'
 import MetadataPanel from './metadata-panel'
@@ -15,21 +16,25 @@ import type { MetadataShape } from '@/app/components/workflow/nodes/knowledge-re
 
 const MetadataTrigger = ({
   metadataFilteringConditions,
-  metadataList = [],
+  metadataList: originalMetadataList = [],
   handleRemoveCondition,
+  selectedDatasetsLoaded,
   ...restProps
 }: MetadataShape) => {
   const { t } = useTranslation()
   const [open, setOpen] = useState(false)
   const conditions = metadataFilteringConditions?.conditions || []
 
+  const metadataList = unionBy(originalMetadataList, 'name').sort(a => a.id === 'built-in' ? 1 : -1)
   useEffect(() => {
-    conditions.forEach((condition) => {
-      if (!metadataList.find(metadata => metadata.name === condition.name))
-        handleRemoveCondition(condition.name)
-    })
+    if (selectedDatasetsLoaded) {
+      conditions.forEach((condition) => {
+        if (!metadataList.find(metadata => metadata.name === condition.name))
+          handleRemoveCondition(condition.name)
+      })
+    }
   // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [metadataList, handleRemoveCondition])
+  }, [metadataList, handleRemoveCondition, selectedDatasetsLoaded])
 
   return (
     <PortalToFollowElem
diff --git a/web/app/components/workflow/nodes/knowledge-retrieval/panel.tsx b/web/app/components/workflow/nodes/knowledge-retrieval/panel.tsx
index f6fb426cac..09d3cdc3f6 100644
--- a/web/app/components/workflow/nodes/knowledge-retrieval/panel.tsx
+++ b/web/app/components/workflow/nodes/knowledge-retrieval/panel.tsx
@@ -37,6 +37,7 @@ const Panel: FC<NodePanelProps<KnowledgeRetrievalNodeType>> = ({
     handleRetrievalModeChange,
     handleMultipleRetrievalConfigChange,
     selectedDatasets,
+    selectedDatasetsLoaded,
     handleOnDatasetsChange,
     isShowSingleRun,
     hideSingleRun,
@@ -130,6 +131,7 @@ const Panel: FC<NodePanelProps<KnowledgeRetrievalNodeType>> = ({
       <div className='mb-2 py-2'>
         <MetadataFilter
           metadataList={metadataList}
+          selectedDatasetsLoaded={selectedDatasetsLoaded}
           metadataFilterMode={inputs.metadata_filtering_mode}
           metadataFilteringConditions={inputs.metadata_filtering_conditions}
           handleAddCondition={handleAddCondition}
diff --git a/web/app/components/workflow/nodes/knowledge-retrieval/types.ts b/web/app/components/workflow/nodes/knowledge-retrieval/types.ts
index f217fa92ea..2331743cae 100644
--- a/web/app/components/workflow/nodes/knowledge-retrieval/types.ts
+++ b/web/app/components/workflow/nodes/knowledge-retrieval/types.ts
@@ -110,6 +110,7 @@ export type HandleToggleConditionLogicalOperator = () => void
 
 export type MetadataShape = {
   metadataList?: MetadataInDoc[]
+  selectedDatasetsLoaded?: boolean
   metadataFilteringConditions?: MetadataFilteringConditions
   handleAddCondition: HandleAddCondition
   handleRemoveCondition: HandleRemoveCondition
diff --git a/web/app/components/workflow/nodes/knowledge-retrieval/use-config.ts b/web/app/components/workflow/nodes/knowledge-retrieval/use-config.ts
index c0454e1bba..b6abe878ed 100644
--- a/web/app/components/workflow/nodes/knowledge-retrieval/use-config.ts
+++ b/web/app/components/workflow/nodes/knowledge-retrieval/use-config.ts
@@ -211,6 +211,7 @@ const useConfig = (id: string, payload: KnowledgeRetrievalNodeType) => {
     setInputs(newInputs)
   }, [inputs, setInputs, selectedDatasets, currentRerankModel, currentRerankProvider])
 
+  const [selectedDatasetsLoaded, setSelectedDatasetsLoaded] = useState(false)
   // datasets
   useEffect(() => {
     (async () => {
@@ -225,6 +226,7 @@ const useConfig = (id: string, payload: KnowledgeRetrievalNodeType) => {
         draft._datasets = selectedDatasets
       })
       setInputs(newInputs)
+      setSelectedDatasetsLoaded(true)
     })()
   // eslint-disable-next-line react-hooks/exhaustive-deps
   }, [])
@@ -418,6 +420,7 @@ const useConfig = (id: string, payload: KnowledgeRetrievalNodeType) => {
     handleModelChanged,
     handleCompletionParamsChange,
     selectedDatasets: selectedDatasets.filter(d => d.name),
+    selectedDatasetsLoaded,
     handleOnDatasetsChange,
     isShowSingleRun,
     hideSingleRun,