diff --git a/packages/ai/src/agents/analyst-agent/analyst-agent.ts b/packages/ai/src/agents/analyst-agent/analyst-agent.ts
index 23ab7f86a..b79c110cc 100644
--- a/packages/ai/src/agents/analyst-agent/analyst-agent.ts
+++ b/packages/ai/src/agents/analyst-agent/analyst-agent.ts
@@ -1,4 +1,5 @@
 import type { PermissionedDataset } from '@buster/access-controls';
+import { waitForPendingUpdates } from '@buster/database/queries';
 import { type ModelMessage, hasToolCall, stepCountIs, streamText } from 'ai';
 import { wrapTraced } from 'braintrust';
 import z from 'zod';
@@ -199,8 +200,10 @@ export function createAnalystAgent(analystAgentOptions: AnalystAgentOptions) {
               hasToolResults: !!event.toolResults,
             });
           },
-          onFinish: () => {
+          onFinish: async () => {
             console.info('Analyst Agent finished');
+            // Ensure all pending database updates complete before stream terminates
+            await waitForPendingUpdates(analystAgentOptions.messageId);
           },
         }),
       {
diff --git a/packages/ai/src/agents/think-and-prep-agent/think-and-prep-agent.ts b/packages/ai/src/agents/think-and-prep-agent/think-and-prep-agent.ts
index cdf89bda9..feac20378 100644
--- a/packages/ai/src/agents/think-and-prep-agent/think-and-prep-agent.ts
+++ b/packages/ai/src/agents/think-and-prep-agent/think-and-prep-agent.ts
@@ -1,4 +1,5 @@
 import type { PermissionedDataset } from '@buster/access-controls';
+import { waitForPendingUpdates } from '@buster/database/queries';
 import { type ModelMessage, hasToolCall, stepCountIs, streamText } from 'ai';
 import { wrapTraced } from 'braintrust';
 import z from 'zod';
@@ -230,6 +231,11 @@ export function createThinkAndPrepAgent(thinkAndPrepAgentSchema: ThinkAndPrepAge
               hasToolResults: !!event.toolResults,
             });
           },
+          onFinish: async () => {
+            console.info('Think and Prep Agent finished');
+            // Ensure all pending database updates complete before stream terminates
+            await waitForPendingUpdates(messageId);
+          },
         }),
       {
         name: 'Think and Prep Agent',
diff --git a/packages/ai/src/tools/communication-tools/done-tool/done-tool-execute.ts b/packages/ai/src/tools/communication-tools/done-tool/done-tool-execute.ts
index 40b2a22b3..fbd7062b7 100644
--- a/packages/ai/src/tools/communication-tools/done-tool/done-tool-execute.ts
+++ b/packages/ai/src/tools/communication-tools/done-tool/done-tool-execute.ts
@@ -1,4 +1,8 @@
-import { updateMessage, updateMessageEntries } from '@buster/database/queries';
+import {
+  updateMessage,
+  updateMessageEntries,
+  waitForPendingUpdates,
+} from '@buster/database/queries';
 import { wrapTraced } from 'braintrust';
 import { cleanupState } from '../../shared/cleanup-state';
 import { createRawToolResultEntry } from '../../shared/create-raw-llm-tool-result-entry';
@@ -57,6 +61,10 @@ export function createDoneToolExecute(context: DoneToolContext, state: DoneToolS
       }
 
       const result = await processDone(state, state.toolCallId, context.messageId, context);
+
+      // Wait for all pending updates from delta/finish to complete before returning
+      await waitForPendingUpdates(context.messageId);
+
       cleanupState(state);
       return result;
     },
diff --git a/packages/database/src/queries/messages/update-message-entries.ts b/packages/database/src/queries/messages/update-message-entries.ts
index 3b56d6d3c..b7f705360 100644
--- a/packages/database/src/queries/messages/update-message-entries.ts
+++ b/packages/database/src/queries/messages/update-message-entries.ts
@@ -24,6 +24,17 @@ export type UpdateMessageEntriesParams = z.infer<typeof UpdateMessageEntriesSche
 // Simple in-memory queue for each messageId
 const updateQueues = new Map<string, Promise<{ success: boolean }>>();
 
+/**
+ * Wait for all pending updates for a given messageId to complete.
+ * This ensures all queued updates are flushed to the database before proceeding.
+ */
+export async function waitForPendingUpdates(messageId: string): Promise<void> {
+  const pendingQueue = updateQueues.get(messageId);
+  if (pendingQueue) {
+    await pendingQueue;
+  }
+}
+
 /**
  * Internal function that performs the actual update logic.
  * This is separated so it can be queued.