diff --git a/src/cli/run/completion.ts b/src/cli/run/completion.ts
index f28927f12..bcc0cebb8 100644
--- a/src/cli/run/completion.ts
+++ b/src/cli/run/completion.ts
@@ -20,6 +20,11 @@ export async function checkCompletionConditions(ctx: RunContext): Promise<boolea
       return false
     }
 
+    if (continuationState.hasActiveBackgroundTaskMarker) {
+      logWaiting(ctx, continuationState.activeHookMarkerReason ?? "background tasks are active")
+      return false
+    }
+
     if (!await areAllChildrenIdle(ctx)) {
       return false
     }
diff --git a/src/cli/run/continuation-state.ts b/src/cli/run/continuation-state.ts
index 07b530812..7e7eb1a6c 100644
--- a/src/cli/run/continuation-state.ts
+++ b/src/cli/run/continuation-state.ts
@@ -16,6 +16,7 @@ export interface ContinuationState {
   hasActiveRalphLoop: boolean
   hasHookMarker: boolean
   hasTodoHookMarker: boolean
+  hasActiveBackgroundTaskMarker: boolean
   hasActiveHookMarker: boolean
   activeHookMarkerReason: string | null
 }
@@ -32,6 +33,7 @@ export async function getContinuationState(
     hasActiveRalphLoop: hasActiveRalphLoopContinuation(directory, sessionID),
     hasHookMarker: marker !== null,
     hasTodoHookMarker: marker?.sources.todo !== undefined,
+    hasActiveBackgroundTaskMarker: marker?.sources["background-task"]?.state === "active",
     hasActiveHookMarker: isContinuationMarkerActive(marker),
     activeHookMarkerReason: getActiveContinuationMarkerReason(marker),
   }
diff --git a/src/features/background-agent/manager.ts b/src/features/background-agent/manager.ts
index a59ea9530..2350d0dbc 100644
--- a/src/features/background-agent/manager.ts
+++ b/src/features/background-agent/manager.ts
@@ -48,6 +48,7 @@ import {
 } from "./error-classifier"
 import { tryFallbackRetry } from "./fallback-retry-handler"
 import { registerManagerForCleanup, unregisterManagerForCleanup } from "./process-cleanup"
+import { setContinuationMarkerSource } from "../../features/run-continuation-state"
 import {
   findNearestMessageExcludingCompaction,
   resolvePromptContextFromSessionMessages,
@@ -370,6 +371,9 @@ export class BackgroundManager {
       spawnReservation.commit()
       this.markPreStartDescendantReservation(task)
 
+      // Signal CLI run mode that background tasks are active
+      this.updateBackgroundTaskMarker(input.parentSessionID)
+
       // Trigger processing (fire-and-forget)
       void this.processKey(key)
 
@@ -657,6 +661,21 @@ export class BackgroundManager {
     return result
   }
 
+  private updateBackgroundTaskMarker(parentSessionID: string): void {
+    const tasks = this.getTasksByParentSession(parentSessionID)
+    const activeTasks = tasks.filter(t => t.status === "running" || t.status === "pending")
+    if (activeTasks.length > 0) {
+      setContinuationMarkerSource(
+        this.directory, parentSessionID, "background-task", "active",
+        `${activeTasks.length} background task(s) active`,
+      )
+    } else {
+      setContinuationMarkerSource(
+        this.directory, parentSessionID, "background-task", "idle",
+      )
+    }
+  }
+
   getAllDescendantTasks(sessionID: string): BackgroundTask[] {
     const result: BackgroundTask[] = []
     const directChildren = this.getTasksByParentSession(sessionID)
@@ -1585,6 +1604,11 @@ export class BackgroundManager {
 
     removeTaskToastTracking(task.id)
 
+    // Update continuation marker for CLI run mode
+    if (task.parentSessionID) {
+      this.updateBackgroundTaskMarker(task.parentSessionID)
+    }
+
     if (options?.skipNotification) {
       this.cleanupPendingByParent(task)
       this.scheduleTaskRemoval(task.id)
@@ -1700,6 +1724,11 @@ export class BackgroundManager {
       SessionCategoryRegistry.remove(task.sessionID)
     }
 
+    // Update continuation marker for CLI run mode
+    if (task.parentSessionID) {
+      this.updateBackgroundTaskMarker(task.parentSessionID)
+    }
+
     try {
       await this.enqueueNotificationForParent(task.parentSessionID, () => this.notifyParentSession(task))
       log(`[background-agent] Task completed via ${source}:`, task.id)
@@ -1993,6 +2022,11 @@ export class BackgroundManager {
       SessionCategoryRegistry.remove(task.sessionID)
     }
 
+    // Update continuation marker for CLI run mode
+    if (task.parentSessionID) {
+      this.updateBackgroundTaskMarker(task.parentSessionID)
+    }
+
     this.markForNotification(task)
     this.enqueueNotificationForParent(task.parentSessionID, () => this.notifyParentSession(task)).catch(err => {
       log("[background-agent] Error in notifyParentSession for crashed task:", { taskId: task.id, error: err })
diff --git a/src/features/run-continuation-state/types.ts b/src/features/run-continuation-state/types.ts
index 856f3d9ef..b851043d3 100644
--- a/src/features/run-continuation-state/types.ts
+++ b/src/features/run-continuation-state/types.ts
@@ -1,4 +1,4 @@
-export type ContinuationMarkerSource = "todo" | "stop"
+export type ContinuationMarkerSource = "todo" | "stop" | "background-task"
 
 export type ContinuationMarkerState = "idle" | "active" | "stopped"
 
diff --git a/src/hooks/todo-continuation-enforcer/continuation-injection.ts b/src/hooks/todo-continuation-enforcer/continuation-injection.ts
index 5844bebd2..d1ca73a1f 100644
--- a/src/hooks/todo-continuation-enforcer/continuation-injection.ts
+++ b/src/hooks/todo-continuation-enforcer/continuation-injection.ts
@@ -79,7 +79,7 @@ export async function injectContinuation(args: {
   }
 
   const hasRunningBgTasks = backgroundManager
-    ? backgroundManager.getTasksByParentSession(sessionID).some((task: { status: string }) => task.status === "running")
+    ? backgroundManager.getTasksByParentSession(sessionID).some((task: { status: string }) => task.status === "running" || task.status === "pending")
     : false
 
   if (hasRunningBgTasks) {
diff --git a/src/hooks/todo-continuation-enforcer/idle-event.ts b/src/hooks/todo-continuation-enforcer/idle-event.ts
index 162b60f6d..2c2c68d45 100644
--- a/src/hooks/todo-continuation-enforcer/idle-event.ts
+++ b/src/hooks/todo-continuation-enforcer/idle-event.ts
@@ -71,7 +71,7 @@ export async function handleSessionIdle(args: {
   }
 
   const hasRunningBgTasks = backgroundManager
-    ? backgroundManager.getTasksByParentSession(sessionID).some((task: { status: string }) => task.status === "running")
+    ? backgroundManager.getTasksByParentSession(sessionID).some((task: { status: string }) => task.status === "running" || task.status === "pending")
     : false
 
   if (hasRunningBgTasks) {