diff --git a/common/build.go b/common/build.go
index ef5dda01..73e7972e 100644
--- a/common/build.go
+++ b/common/build.go
@@ -656,11 +656,8 @@ func (b *Build) executeStage(ctx context.Context, buildStage BuildStage, executo
 			// rather than the returned error because gRPC wraps deadline
 			// exceeded as a status error that does not unwrap to
 			// context.DeadlineExceeded.
-			if err != nil && errors.Is(ctx.Err(), context.DeadlineExceeded) {
-				b.logger.Warningln(
-					string(buildStage) + " could not run to completion because the timeout was exceeded. " +
-						"For more control over job and script timeouts see: " +
-						"https://docs.gitlab.com/ci/runners/configure_runners/#set-script-and-after_script-timeouts")
+			if err != nil {
+				b.warnTimeoutExceeded(ctx, string(buildStage))
 			}
 			return err
 		}
@@ -676,14 +673,7 @@ func (b *Build) executeStage(ctx context.Context, buildStage BuildStage, executo
 	b.setCurrentStage(buildStage)
 	b.Log().WithField("build_stage", buildStage).Debug("Executing build stage")
 
-	defer func() {
-		if errors.Is(ctx.Err(), context.DeadlineExceeded) {
-			b.logger.Warningln(
-				string(buildStage) + " could not run to completion because the timeout was exceeded. " +
-					"For more control over job and script timeouts see: " +
-					"https://docs.gitlab.com/ci/runners/configure_runners/#set-script-and-after_script-timeouts")
-		}
-	}()
+	defer b.warnTimeoutExceeded(ctx, string(buildStage))
 
 	shell := executor.Shell()
 	if shell == nil {
@@ -828,6 +818,12 @@ func (b *Build) executeScript(ctx context.Context, trace JobTrace, executor Exec
 		//nolint:errcheck
 		err = b.executeStepStage(ctx, executor.(steps.Connector), "concrete", concreteSteps, trace.SetCancelFunc)
 
+		// Whole-job dispatch: stage breakdown isn't visible to the user, so
+		// attribute the timeout to "Job" rather than a build stage.
+		if err != nil {
+			b.warnTimeoutExceeded(ctx, "Job")
+		}
+
 		b.executeUploadReferees(ctx, startTime, time.Now())
 
 		return err
@@ -1092,6 +1088,16 @@ func (b *Build) attemptExecuteStage(
 	return err
 }
 
+func (b *Build) warnTimeoutExceeded(ctx context.Context, subject string) {
+	if !errors.Is(ctx.Err(), context.DeadlineExceeded) {
+		return
+	}
+	b.logger.Warningln(
+		subject + " could not run to completion because the timeout was exceeded. " +
+			"For more control over job and script timeouts see: " +
+			"https://docs.gitlab.com/ci/runners/configure_runners/#set-script-and-after_script-timeouts")
+}
+
 func (b *Build) GetBuildTimeout() time.Duration {
 	buildTimeout := b.RunnerInfo.Timeout
 	if buildTimeout <= 0 {
diff --git a/functions/concrete/builder/builder.go b/functions/concrete/builder/builder.go
index 310ae0fd..30fba029 100644
--- a/functions/concrete/builder/builder.go
+++ b/functions/concrete/builder/builder.go
@@ -353,7 +353,6 @@ func (b *builder) buildSteps() []stages.Step {
 		})
 
 		if step.Name == spec.StepNameAfterScript {
-			s.AllowFailure = true
 			s.OnSuccess = true
 			s.OnFailure = true
 			afterScript = append(afterScript, s)
diff --git a/functions/concrete/run/runner.go b/functions/concrete/run/runner.go
index d17b3d62..cbfc5c64 100644
--- a/functions/concrete/run/runner.go
+++ b/functions/concrete/run/runner.go
@@ -224,17 +224,21 @@ func (r *Runner) runScriptSteps(jobCtx context.Context, steps []stages.Step) err
 	r.setCancel(cancel)
 
 	var firstErr error
+	timeoutStage := "step_script"
 	for _, step := range steps {
 		r.loadGitlabEnv()
 
-		if err := r.section(scriptCtx, "step_"+step.Step, step.Run); err != nil {
+		sectionName := "step_" + step.Step
+		if err := r.section(scriptCtx, sectionName, step.Run); err != nil {
 			if firstErr == nil {
 				firstErr = err
 			}
+			timeoutStage = sectionName
 			break
 		}
 	}
 
+	r.warnStageTimeout(jobCtx, scriptCtx, timeoutStage)
 	return r.classifyScriptContextError(jobCtx, scriptCtx, firstErr)
 }
 
@@ -277,6 +281,7 @@ func (r *Runner) runAfterScriptSteps(jobCtx context.Context, steps []stages.Step
 		return nil
 	})
 
+	r.warnStageTimeout(jobCtx, afterCtx, "after_script")
 	return err
 }
 
@@ -386,6 +391,21 @@ func (r *Runner) logWarningf(format string, args ...interface{}) {
 	fmt.Fprintf(r.env.Stderr, " %s\033[0m\n", msg)
 }
 
+// warnStageTimeout fires only on a stage-only deadline; the job-level
+// case is owned by the outer runner.
+func (r *Runner) warnStageTimeout(jobCtx, stageCtx context.Context, stageName string) {
+	if !errors.Is(stageCtx.Err(), context.DeadlineExceeded) {
+		return
+	}
+	if errors.Is(jobCtx.Err(), context.DeadlineExceeded) {
+		return
+	}
+	r.logWarningf("%s could not run to completion because the timeout was exceeded. "+
+		"For more control over job and script timeouts see: "+
+		"https://docs.gitlab.com/ci/runners/configure_runners/#set-script-and-after_script-timeouts",
+		stageName)
+}
+
 // setupGitlabEnv creates the GITLAB_ENV file so user scripts can append
 // KEY=VALUE lines to define dynamic variables for subsequent steps.
 func (r *Runner) setupGitlabEnv() error {