diff --git a/apps/desktop/src/app/session/hooks/use-message-stream/gateway-event.ts b/apps/desktop/src/app/session/hooks/use-message-stream/gateway-event.ts
index 4e0a439219ca..eb99e1fbd895 100644
--- a/apps/desktop/src/app/session/hooks/use-message-stream/gateway-event.ts
+++ b/apps/desktop/src/app/session/hooks/use-message-stream/gateway-event.ts
@@ -47,8 +47,10 @@ import {
   setTurnStartedAt,
   setYoloActive
 } from '@/store/session'
-import { clearSessionSubagents, pruneDelegateFallbackSubagents, upsertSubagent } from '@/store/subagents'
+import { broadcastSessionsChanged } from '@/store/session-sync'
 import { clearActiveSessionTodos } from '@/store/todos'
+import { clearSessionSubagents, pruneDelegateFallbackSubagents, pruneFinishedSessionSubagents, upsertSubagent } from '@/store/subagents'
+import { setSessionTodos } from '@/store/todos'
 import { recordToolDiff } from '@/store/tool-diffs'
 import { reportInstallMethodWarning } from '@/store/updates'
 import { notifyWorkspaceChanged, toolChangedPath, toolMayMutateFiles } from '@/store/workspace-events'
@@ -439,7 +441,7 @@ export function useGatewayEventHandler(deps: GatewayEventDeps) {
         }
 
         flushQueuedDeltas(sessionId)
-        clearSessionSubagents(sessionId)
+        pruneFinishedSessionSubagents(sessionId)
         setSessionCompacting(sessionId, false)
         compactedTurnRef.current.delete(sessionId)
         nativeSubagentSessionsRef.current.delete(sessionId)
diff --git a/apps/desktop/src/store/subagents.test.ts b/apps/desktop/src/store/subagents.test.ts
index c0b87ba58eae..51c752ddea22 100644
--- a/apps/desktop/src/store/subagents.test.ts
+++ b/apps/desktop/src/store/subagents.test.ts
@@ -8,6 +8,7 @@ import {
   clearSessionSubagents,
   failedSubagentCount,
   pruneDelegateFallbackSubagents,
+  pruneFinishedSessionSubagents,
   upsertSubagent
 } from './subagents'
 
@@ -131,4 +132,55 @@ describe('subagent store', () => {
     expect($subagentsBySession.get().s1).toBeUndefined()
     expect($subagentsBySession.get().s2).toHaveLength(1)
   })
+
+  // Regression test for #64015: still-RUNNING background subagents must survive
+  // the per-turn wipe that previously dropped them at message.start. The fix
+  // replaces clearSessionSubagents() with pruneFinishedSessionSubagents() at
+  // the use-message-stream message.start handler, so only terminal-status rows
+  // get filtered out.
+  it('pruneFinishedSessionSubagents keeps running/queued and drops terminal rows', () => {
+    upsertSubagent('s1', { goal: 'live-a', status: 'running', subagent_id: 'live-a', task_index: 0 })
+    upsertSubagent('s1', { goal: 'live-b', status: 'queued', subagent_id: 'live-b', task_index: 1 })
+    upsertSubagent('s1', { goal: 'done', status: 'completed', subagent_id: 'done', task_index: 2 })
+    upsertSubagent('s1', { goal: 'broken', status: 'failed', subagent_id: 'broken', task_index: 3 })
+    upsertSubagent('s1', { goal: 'cancelled', status: 'interrupted', subagent_id: 'cancelled', task_index: 4 })
+
+    pruneFinishedSessionSubagents('s1')
+
+    const ids = listFor('s1').map(item => item.id).sort()
+    expect(ids).toEqual(['live-a', 'live-b'])
+    expect(activeSubagentCount(listFor('s1'))).toBe(2)
+  })
+
+  // Companion test: after prune, a late `subagent.complete` event for a
+  // surviving live row must still be accepted by upsertSubagent (the wipe
+  // path previously silently dropped these).
+  it('surviving live subagents still accept createIfMissing=false completion', () => {
+    upsertSubagent('s1', { goal: 'live', status: 'running', subagent_id: 'live', task_index: 0 })
+
+    pruneFinishedSessionSubagents('s1')
+
+    upsertSubagent(
+      's1',
+      { status: 'completed', subagent_id: 'live', task_index: 0, summary: 'finished later' },
+      false,
+      'subagent.complete'
+    )
+
+    const item = listFor('s1')[0]
+    expect(item?.status).toBe('completed')
+    expect(item?.summary).toBe('finished later')
+  })
+
+  it('pruneFinishedSessionSubagents leaves other sessions untouched', () => {
+    upsertSubagent('s1', { goal: 'live', status: 'running', subagent_id: 'a', task_index: 0 })
+    upsertSubagent('s1', { goal: 'done', status: 'completed', subagent_id: 'b', task_index: 1 })
+    upsertSubagent('s2', { goal: 'live', status: 'running', subagent_id: 'c', task_index: 0 })
+    upsertSubagent('s2', { goal: 'done', status: 'completed', subagent_id: 'd', task_index: 1 })
+
+    pruneFinishedSessionSubagents('s1')
+
+    expect(listFor('s1').map(item => item.id)).toEqual(['a'])
+    expect(listFor('s2').map(item => item.id).sort()).toEqual(['c', 'd'])
+  })
 })
diff --git a/apps/desktop/src/store/subagents.ts b/apps/desktop/src/store/subagents.ts
index e54f3fc169b2..6127b15183c2 100644
--- a/apps/desktop/src/store/subagents.ts
+++ b/apps/desktop/src/store/subagents.ts
@@ -189,6 +189,35 @@ export function clearSessionSubagents(sid: string) {
   $subagentsBySession.set(rest)
 }
 
+/**
+ * Prune terminal-status subagent rows for a session, leaving running/queued
+ * entries untouched. Used at the `message.start` boundary in the desktop
+ * message-stream hook so that the *previous* turn's finished rows get flushed
+ * from the display while background subagents that outlived the spawning turn
+ * remain visible (and still accept late progress/complete events).
+ *
+ * Distinct from `clearSessionSubagents` (used by the Stop action, which
+ * genuinely cancels running subagents and so should drop them all) and from
+ * `pruneDelegateFallbackSubagents` (which filters by id prefix to remove
+ * placeholder rows once the real native event arrives).
+ */
+export function pruneFinishedSessionSubagents(sid: string) {
+  const map = $subagentsBySession.get()
+  const list = map[sid]
+
+  if (!list?.length) {
+    return
+  }
+
+  const next = list.filter(item => item.status === 'running' || item.status === 'queued')
+
+  if (next.length === list.length) {
+    return
+  }
+
+  $subagentsBySession.set({ ...map, [sid]: next })
+}
+
 export function pruneDelegateFallbackSubagents(sid: string) {
   const map = $subagentsBySession.get()
   const list = map[sid]