diff --git a/packages/server/src/utils/buildAgentflow.test.ts b/packages/server/src/utils/buildAgentflow.test.ts
new file mode 100644
index 00000000000..3b4f94f9136
--- /dev/null
+++ b/packages/server/src/utils/buildAgentflow.test.ts
@@ -0,0 +1,72 @@
+import { findChatMessageActionToClear } from './buildAgentflow'
+import { ChatMessage } from '../database/entities/ChatMessage'
+
+const makeMessage = (id: string, action: object | null): ChatMessage => {
+    const message = new ChatMessage()
+    message.id = id
+    message.action = action ? JSON.stringify(action) : null
+    return message
+}
+
+describe('findChatMessageActionToClear', () => {
+    it('returns the message whose action.data.nodeId matches the resumed startNodeId', () => {
+        const messages = [
+            makeMessage('msg-3', { data: { nodeId: 'humanInput_2' } }),
+            makeMessage('msg-2', { data: { nodeId: 'humanInput_1' } }),
+            makeMessage('msg-1', null)
+        ]
+
+        const result = findChatMessageActionToClear(messages, 'humanInput_1')
+
+        expect(result?.id).toBe('msg-2')
+    })
+
+    it('does not clear a different pending Human-In-The-Loop node just because it is newer (#4787)', () => {
+        // Two HIL nodes are pending at the same time. Resuming humanInput_1 must not touch
+        // the chat message that belongs to humanInput_2, even though it was created more recently.
+        const newerUnrelatedAction = makeMessage('msg-newer', { data: { nodeId: 'humanInput_2' } })
+        const olderTargetAction = makeMessage('msg-older', { data: { nodeId: 'humanInput_1' } })
+        const messages = [newerUnrelatedAction, olderTargetAction]
+
+        const result = findChatMessageActionToClear(messages, 'humanInput_1')
+
+        expect(result?.id).toBe('msg-older')
+        expect(result?.id).not.toBe(newerUnrelatedAction.id)
+    })
+
+    it('returns undefined when no message matches the startNodeId', () => {
+        const messages = [makeMessage('msg-1', { data: { nodeId: 'humanInput_2' } })]
+
+        const result = findChatMessageActionToClear(messages, 'humanInput_1')
+
+        expect(result).toBeUndefined()
+    })
+
+    it('returns undefined when startNodeId is not provided', () => {
+        const messages = [makeMessage('msg-1', { data: { nodeId: 'humanInput_1' } })]
+
+        const result = findChatMessageActionToClear(messages, undefined)
+
+        expect(result).toBeUndefined()
+    })
+
+    it('skips messages with malformed action JSON instead of throwing', () => {
+        const malformed = new ChatMessage()
+        malformed.id = 'msg-malformed'
+        malformed.action = '{not valid json'
+
+        const valid = makeMessage('msg-valid', { data: { nodeId: 'humanInput_1' } })
+
+        const result = findChatMessageActionToClear([malformed, valid], 'humanInput_1')
+
+        expect(result?.id).toBe('msg-valid')
+    })
+
+    it('skips messages with no action set', () => {
+        const messages = [makeMessage('msg-1', null), makeMessage('msg-2', { data: { nodeId: 'humanInput_1' } })]
+
+        const result = findChatMessageActionToClear(messages, 'humanInput_1')
+
+        expect(result?.id).toBe('msg-2')
+    })
+})
diff --git a/packages/server/src/utils/buildAgentflow.ts b/packages/server/src/utils/buildAgentflow.ts
index e38ccbec092..af25efd0f5c 100644
--- a/packages/server/src/utils/buildAgentflow.ts
+++ b/packages/server/src/utils/buildAgentflow.ts
@@ -2313,7 +2313,8 @@ export const executeAgentFlow = async ({
         }
     }
 
-    // Find the previous chat message with the same session/chat id and remove the action
+    // Clear the action on the specific message tied to the resumed node (not just the newest
+    // pending action) - a flow can have multiple HIL nodes pending at once. See #4787.
     if (humanInput && Object.keys(humanInput).length) {
         let query = await appDataSource
             .getRepository(ChatMessage)
@@ -2323,19 +2324,13 @@ export const executeAgentFlow = async ({
             .orderBy('chat_message.createdDate', 'DESC')
             .getMany()
 
-        for (const result of query) {
-            if (result.action) {
-                try {
-                    const newChatMessage = new ChatMessage()
-                    Object.assign(newChatMessage, result)
-                    newChatMessage.action = null
-                    const cm = await appDataSource.getRepository(ChatMessage).create(newChatMessage)
-                    await appDataSource.getRepository(ChatMessage).save(cm)
-                    break
-                } catch (e) {
-                    // error converting action to JSON
-                }
-            }
+        const messageToClear = findChatMessageActionToClear(query, humanInput.startNodeId)
+        if (messageToClear) {
+            const newChatMessage = new ChatMessage()
+            Object.assign(newChatMessage, messageToClear)
+            newChatMessage.action = null
+            const cm = await appDataSource.getRepository(ChatMessage).create(newChatMessage)
+            await appDataSource.getRepository(ChatMessage).save(cm)
         }
     }
 
@@ -2469,3 +2464,21 @@ export const executeAgentFlow = async ({
 export const isObjectNotEmpty = (obj: any): boolean => {
     return obj && Object.keys(obj).length > 0 && obj.constructor === Object
 }
+
+/**
+ * Finds the chat message whose pending action belongs to the given (resumed) HIL node.
+ * Matches by nodeId instead of recency, since multiple HIL nodes can be pending at once. See #4787.
+ */
+export const findChatMessageActionToClear = (messages: ChatMessage[], startNodeId?: string): ChatMessage | undefined => {
+    if (!startNodeId) return undefined
+    for (const message of messages) {
+        if (!message.action) continue
+        try {
+            const parsedAction = JSON.parse(message.action)
+            if (parsedAction?.data?.nodeId === startNodeId) return message
+        } catch (e) {
+            // error converting action to JSON, skip this message
+        }
+    }
+    return undefined
+}
diff --git a/packages/ui/src/views/chatmessage/ChatMessage.jsx b/packages/ui/src/views/chatmessage/ChatMessage.jsx
index bf55a262022..c2303fc16e8 100644
--- a/packages/ui/src/views/chatmessage/ChatMessage.jsx
+++ b/packages/ui/src/views/chatmessage/ChatMessage.jsx
@@ -889,8 +889,12 @@ const ChatMessage = ({ open, chatflowid, isAgentCanvas, isDialog, previews, setP
         setUserInput(elem.label)
         setMessages((prevMessages) => {
             let allMessages = [...cloneDeep(prevMessages)]
-            if (allMessages[allMessages.length - 1].type === 'userMessage') return allMessages
-            allMessages[allMessages.length - 1].action = null
+            // Clear the action on the message this button belongs to, not just the last message - a flow
+            // can have multiple pending HIL nodes at once. See #4787.
+            const targetIndex = allMessages.findIndex((msg) => msg.action && action && msg.action.id === action.id)
+            const indexToClear = targetIndex !== -1 ? targetIndex : allMessages.length - 1
+            if (allMessages[indexToClear].type === 'userMessage') return allMessages
+            allMessages[indexToClear].action = null
             return allMessages
         })
         if (elem.type.includes('agentflowv2')) {