diff --git a/pkg/reconciler/pipelinerun/pipelinerun.go b/pkg/reconciler/pipelinerun/pipelinerun.go
index 6f40fff9ece..b3b89f1dcc3 100644
--- a/pkg/reconciler/pipelinerun/pipelinerun.go
+++ b/pkg/reconciler/pipelinerun/pipelinerun.go
@@ -1331,20 +1331,32 @@ func (c *Reconciler) updatePipelineRunStatusFromInformer(ctx context.Context, pr
 
 func updatePipelineRunStatusFromChildObjects(ctx context.Context, logger *zap.SugaredLogger, pr *v1beta1.PipelineRun, taskRuns []*v1beta1.TaskRun, runObjects []v1beta1.RunObject) error {
 	cfg := config.FromContextOrDefaults(ctx)
-	fullEmbedded := cfg.FeatureFlags.EmbeddedStatus == config.FullEmbeddedStatus || cfg.FeatureFlags.EmbeddedStatus == config.BothEmbeddedStatus
-	minimalEmbedded := cfg.FeatureFlags.EmbeddedStatus == config.MinimalEmbeddedStatus || cfg.FeatureFlags.EmbeddedStatus == config.BothEmbeddedStatus
 
-	if minimalEmbedded {
-		updatePipelineRunStatusFromChildRefs(logger, pr, taskRuns, runObjects)
-	}
-	if fullEmbedded {
+	switch cfg.FeatureFlags.EmbeddedStatus {
+	case config.FullEmbeddedStatus:
+		// Clear any ChildReferences that are present.
+		// This can occur if the value of "embedded-status" was modified during PipelineRun execution.
+		pr.Status.ChildReferences = nil
+		updatePipelineRunStatusFromTaskRuns(logger, pr, taskRuns)
+		updatePipelineRunStatusFromCustomRunsOrRuns(logger, pr, runObjects)
+	case config.BothEmbeddedStatus:
 		updatePipelineRunStatusFromTaskRuns(logger, pr, taskRuns)
 		updatePipelineRunStatusFromCustomRunsOrRuns(logger, pr, runObjects)
+		updatePipelineRunStatusFromChildRefs(logger, pr, taskRuns, runObjects)
+	default:
+		// Clear any TaskRuns and Runs present in the status.
+		// This can occur if the value of "embedded-status" was modified during PipelineRun execution.
+		pr.Status.Runs = nil
+		pr.Status.TaskRuns = nil
+		updatePipelineRunStatusFromChildRefs(logger, pr, taskRuns, runObjects)
 	}
 
 	return validateChildObjectsInPipelineRunStatus(ctx, pr.Status)
 }
 
+// TODO: https://github.com/tektoncd/pipeline/issues/5999 integration tests for changing
+// feature flags could help prevent validation errors when the feature-flag is being switched.
+// In such case, the error could keep the pipelineRun run indefinitely.
 func validateChildObjectsInPipelineRunStatus(ctx context.Context, prs v1beta1.PipelineRunStatus) error {
 	cfg := config.FromContextOrDefaults(ctx)
 
diff --git a/pkg/reconciler/pipelinerun/pipelinerun_test.go b/pkg/reconciler/pipelinerun/pipelinerun_test.go
index 074ff102495..e7602c7c0e5 100644
--- a/pkg/reconciler/pipelinerun/pipelinerun_test.go
+++ b/pkg/reconciler/pipelinerun/pipelinerun_test.go
@@ -5161,7 +5161,7 @@ status:
 		expectedPr = expectedPrMinimalStatus
 	}
 
-	if d := cmp.Diff(expectedPr, reconciledRun, ignoreResourceVersion, ignoreLastTransitionTime, ignoreCompletionTime, ignoreStartTime); d != "" {
+	if d := cmp.Diff(expectedPr, reconciledRun, ignoreResourceVersion, ignoreLastTransitionTime, ignoreCompletionTime, ignoreStartTime, cmpopts.EquateEmpty()); d != "" {
 		t.Errorf("expected to see pipeline run results created. Diff %s", diff.PrintWantGot(d))
 	}
 }
@@ -5482,7 +5482,7 @@ status:
 		expectedPr = expectedPrMinimalStatus
 	}
 
-	if d := cmp.Diff(expectedPr, reconciledRun, ignoreResourceVersion, ignoreLastTransitionTime, ignoreCompletionTime, ignoreStartTime); d != "" {
+	if d := cmp.Diff(expectedPr, reconciledRun, ignoreResourceVersion, ignoreLastTransitionTime, ignoreCompletionTime, ignoreStartTime, cmpopts.EquateEmpty()); d != "" {
 		t.Errorf("expected to see pipeline run results created. Diff %s", diff.PrintWantGot(d))
 	}
 }
@@ -8947,7 +8947,7 @@ spec:
 			if err != nil {
 				t.Fatalf("Got an error getting reconciled run out of fake client: %s", err)
 			}
-			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime); d != "" {
+			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime, cmpopts.EquateEmpty()); d != "" {
 				t.Errorf("expected PipelineRun was not created. Diff %s", diff.PrintWantGot(d))
 			}
 		})
@@ -9555,7 +9555,7 @@ spec:
 			if err != nil {
 				t.Fatalf("Got an error getting reconciled run out of fake client: %s", err)
 			}
-			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime); d != "" {
+			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime, cmpopts.EquateEmpty()); d != "" {
 				t.Errorf("expected PipelineRun was not created. Diff %s", diff.PrintWantGot(d))
 			}
 		})
@@ -10015,7 +10015,7 @@ status:
 			if err != nil {
 				t.Fatalf("Got an error getting reconciled run out of fake client: %s", err)
 			}
-			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, cmpopts.SortSlices(lessChildReferences)); d != "" {
+			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, cmpopts.SortSlices(lessChildReferences), cmpopts.EquateEmpty()); d != "" {
 				t.Errorf("expected PipelineRun was not created. Diff %s", diff.PrintWantGot(d))
 			}
 		})
@@ -10549,7 +10549,7 @@ spec:
 			if err != nil {
 				t.Fatalf("Got an error getting reconciled run out of fake client: %s", err)
 			}
-			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime); d != "" {
+			if d := cmp.Diff(tt.expectedPipelineRun, pipelineRun, ignoreResourceVersion, ignoreTypeMeta, ignoreLastTransitionTime, ignoreStartTime, ignoreFinallyStartTime, cmpopts.EquateEmpty()); d != "" {
 				t.Errorf("expected PipelineRun was not created. Diff %s", diff.PrintWantGot(d))
 			}
 		})