diff --git a/sdks/go/pkg/beam/runners/prism/internal/jobservices/management.go b/sdks/go/pkg/beam/runners/prism/internal/jobservices/management.go
index 3efe48e23119..7676d958031c 100644
--- a/sdks/go/pkg/beam/runners/prism/internal/jobservices/management.go
+++ b/sdks/go/pkg/beam/runners/prism/internal/jobservices/management.go
@@ -180,12 +180,21 @@ func (s *Server) Prepare(ctx context.Context, req *jobpb.PrepareJobRequest) (*jo
 
 		default:
 			// Composites can often have some unknown urn, permit those.
-			// Eg. The Python SDK has urns "beam:transform:generic_composite:v1", "beam:transform:pickled_python:v1", as well as the deprecated "beam:transform:read:v1",
-			// but they are composites. Since we don't do anything special with the high level, we simply use their internal subgraph.
+			// Eg. The Python SDK has urns "beam:transform:generic_composite:v1", "beam:transform:pickled_python:v1",
+			// as well as the deprecated "beam:transform:read:v1", but they are composites.
+			// We don't do anything special with these high level composites, but
+			// we may be dealing with their internal subgraph already, so we ignore this transform.
 			if len(t.GetSubtransforms()) > 0 {
 				continue
 			}
-			// But if not, fail.
+			// This may be an "empty" composite without subtransforms or a payload.
+			// These just do PCollection manipulation which is already represented in the Pipeline graph.
+			// Simply ignore the composite at this stage, since the runner does nothing with them.
+			if len(t.GetSpec().GetPayload()) == 0 {
+				continue
+			}
+			// Otherwise fail.
+			slog.Warn("unknown transform, with payload", "urn", urn, "name", t.GetUniqueName(), "payload", t.GetSpec().GetPayload())
 			check("PTransform.Spec.Urn", urn+" "+t.GetUniqueName(), "<doesn't exist>")
 		}
 	}