diff --git a/go/oasis-test-runner/scenario/e2e/runtime/runtime_dynamic.go b/go/oasis-test-runner/scenario/e2e/runtime/runtime_dynamic.go
index 296318cde67..9596a7b1074 100644
--- a/go/oasis-test-runner/scenario/e2e/runtime/runtime_dynamic.go
+++ b/go/oasis-test-runner/scenario/e2e/runtime/runtime_dynamic.go
@@ -250,6 +250,12 @@ func (sc *runtimeDynamicImpl) Run(childEnv *env.Env) error { // nolint: gocyclo
 		}
 	}
 
+	// Perform an epoch transition to make sure all nodes are eligible. They may not be eligible
+	// if they have registered after the beacon commit phase.
+	if err := sc.epochTransition(ctx); err != nil {
+		return err
+	}
+
 	for i := 0; i < 5; i++ {
 		// Perform another epoch transition to elect compute runtime committees.
 		if err := sc.epochTransition(ctx); err != nil {
@@ -361,6 +367,12 @@ func (sc *runtimeDynamicImpl) Run(childEnv *env.Env) error { // nolint: gocyclo
 		}
 	}
 
+	// Perform an epoch transition to make sure all nodes are eligible. They may not be eligible
+	// if they have registered after the beacon commit phase.
+	if err = sc.epochTransition(ctx); err != nil {
+		return err
+	}
+
 	// Epoch transition.
 	if err = sc.epochTransition(ctx); err != nil {
 		return err