diff --git a/src/transform/single_entry_point.cc b/src/transform/single_entry_point.cc
index da9c273..fb99663 100644
--- a/src/transform/single_entry_point.cc
+++ b/src/transform/single_entry_point.cc
@@ -105,6 +105,11 @@
 
   // Clone the entry point.
   ctx.dst->AST().AddFunction(ctx.Clone(entry_point));
+
+  // Retain the list of applied transforms.
+  // We need to do this manually since we are not going to use the top-level
+  // ctx.Clone() function.
+  ctx.dst->SetTransformApplied(ctx.src->TransformsApplied());
 }
 
 SingleEntryPoint::Config::Config(std::string entry_point)