diff --git a/pkg/reconciler/pipelinerun/timeout.go b/pkg/reconciler/pipelinerun/timeout.go
index 32a1da8ae7d..8ae29a62d30 100644
--- a/pkg/reconciler/pipelinerun/timeout.go
+++ b/pkg/reconciler/pipelinerun/timeout.go
@@ -27,6 +27,7 @@ import (
 	"go.uber.org/zap"
 	"gomodules.xyz/jsonpatch/v2"
 	corev1 "k8s.io/api/core/v1"
+	"k8s.io/apimachinery/pkg/api/errors"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/apimachinery/pkg/types"
 	"k8s.io/apimachinery/pkg/util/sets"
@@ -92,6 +93,17 @@ func timeoutPipelineRun(ctx context.Context, logger *zap.SugaredLogger, pr *v1.P
 
 func timeoutCustomRun(ctx context.Context, customRunName string, namespace string, clientSet clientset.Interface) error {
 	_, err := clientSet.TektonV1beta1().CustomRuns(namespace).Patch(ctx, customRunName, types.JSONPatchType, timeoutCustomRunPatchBytes, metav1.PatchOptions{}, "")
+	if errors.IsNotFound(err) {
+		return nil
+	}
+	return err
+}
+
+func timeoutTaskRun(ctx context.Context, taskRunName string, namespace string, clientSet clientset.Interface) error {
+	_, err := clientSet.TektonV1().TaskRuns(namespace).Patch(ctx, taskRunName, types.JSONPatchType, timeoutTaskRunPatchBytes, metav1.PatchOptions{}, "")
+	if errors.IsNotFound(err) {
+		return nil
+	}
 	return err
 }
 
@@ -112,7 +124,7 @@ func timeoutPipelineTasksForTaskNames(ctx context.Context, logger *zap.SugaredLo
 	for _, taskRunName := range trNames {
 		logger.Infof("patching TaskRun %s for timeout", taskRunName)
 
-		if _, err := clientSet.TektonV1().TaskRuns(pr.Namespace).Patch(ctx, taskRunName, types.JSONPatchType, timeoutTaskRunPatchBytes, metav1.PatchOptions{}, ""); err != nil {
+		if err := timeoutTaskRun(ctx, taskRunName, pr.Namespace, clientSet); err != nil {
 			errs = append(errs, fmt.Errorf("failed to patch TaskRun `%s` with timeout: %w", taskRunName, err).Error())
 			continue
 		}
diff --git a/pkg/reconciler/pipelinerun/timeout_test.go b/pkg/reconciler/pipelinerun/timeout_test.go
index 0b65cf08f35..a369aeee268 100644
--- a/pkg/reconciler/pipelinerun/timeout_test.go
+++ b/pkg/reconciler/pipelinerun/timeout_test.go
@@ -59,6 +59,23 @@ func TestTimeoutPipelineRun(t *testing.T) {
 		taskRuns: []*v1.TaskRun{
 			{ObjectMeta: metav1.ObjectMeta{Name: "t1"}},
 		},
+	}, {
+		name: "multiple-runs-missing",
+		pipelineRun: &v1.PipelineRun{
+			ObjectMeta: metav1.ObjectMeta{Name: "test-pipeline-run-timedout"},
+			Spec:       v1.PipelineRunSpec{},
+			Status: v1.PipelineRunStatus{PipelineRunStatusFields: v1.PipelineRunStatusFields{
+				ChildReferences: []v1.ChildStatusReference{{
+					TypeMeta:         runtime.TypeMeta{Kind: taskRun},
+					Name:             "t1",
+					PipelineTaskName: "task-1",
+				}, {
+					TypeMeta:         runtime.TypeMeta{Kind: customRun},
+					Name:             "t2",
+					PipelineTaskName: "task-2",
+				}},
+			}},
+		},
 	}, {
 		name: "multiple-taskruns",
 		pipelineRun: &v1.PipelineRun{