diff --git a/include/tint/tint.h b/include/tint/tint.h
index 7b55fe2ac3..d8c52336c3 100644
--- a/include/tint/tint.h
+++ b/include/tint/tint.h
@@ -25,7 +25,6 @@
 #include "src/reader/reader.h"
 #include "src/transform/binding_remapper.h"
 #include "src/transform/bound_array_accessors.h"
-#include "src/transform/canonicalize_entry_point_io.h"
 #include "src/transform/emit_vertex_point_size.h"
 #include "src/transform/first_index_offset.h"
 #include "src/transform/manager.h"
diff --git a/samples/main.cc b/samples/main.cc
index f31d8add7d..2f9f7b82ed 100644
--- a/samples/main.cc
+++ b/samples/main.cc
@@ -701,15 +701,11 @@ int main(int argc, const char** argv) {
 #endif  // TINT_BUILD_SPV_WRITER
 #if TINT_BUILD_MSL_WRITER
     case Format::kMsl:
-      transform_manager.append(
-          std::make_unique<tint::transform::CanonicalizeEntryPointIO>());
       transform_manager.append(std::make_unique<tint::transform::Msl>());
       break;
 #endif  // TINT_BUILD_MSL_WRITER
 #if TINT_BUILD_HLSL_WRITER
     case Format::kHlsl:
-      transform_manager.append(
-          std::make_unique<tint::transform::CanonicalizeEntryPointIO>());
       transform_manager.append(std::make_unique<tint::transform::Hlsl>());
       break;
 #endif  // TINT_BUILD_HLSL_WRITER
diff --git a/src/transform/hlsl.cc b/src/transform/hlsl.cc
index 0fdddc9931..d2af5059b5 100644
--- a/src/transform/hlsl.cc
+++ b/src/transform/hlsl.cc
@@ -23,6 +23,7 @@
 #include "src/semantic/statement.h"
 #include "src/semantic/variable.h"
 #include "src/transform/calculate_array_length.h"
+#include "src/transform/canonicalize_entry_point_io.h"
 #include "src/transform/decompose_storage_access.h"
 #include "src/transform/manager.h"
 
@@ -34,6 +35,7 @@ Hlsl::~Hlsl() = default;
 
 Transform::Output Hlsl::Run(const Program* in, const DataMap& data) {
   Manager manager;
+  manager.Add<CanonicalizeEntryPointIO>();
   manager.Add<DecomposeStorageAccess>();
   manager.Add<CalculateArrayLength>();
   auto out = manager.Run(in, data);
diff --git a/src/transform/msl.cc b/src/transform/msl.cc
index af4bc448e6..48cebce7c0 100644
--- a/src/transform/msl.cc
+++ b/src/transform/msl.cc
@@ -17,6 +17,8 @@
 #include <utility>
 
 #include "src/program_builder.h"
+#include "src/transform/canonicalize_entry_point_io.h"
+#include "src/transform/manager.h"
 
 namespace tint {
 namespace transform {
@@ -262,12 +264,19 @@ const char* kReservedKeywords[] = {"access",
 Msl::Msl() = default;
 Msl::~Msl() = default;
 
-Transform::Output Msl::Run(const Program* in, const DataMap&) {
-  ProgramBuilder out;
-  CloneContext ctx(&out, in);
+Transform::Output Msl::Run(const Program* in, const DataMap& data) {
+  Manager manager;
+  manager.Add<CanonicalizeEntryPointIO>();
+  auto out = manager.Run(in, data);
+  if (!out.program.IsValid()) {
+    return out;
+  }
+
+  ProgramBuilder builder;
+  CloneContext ctx(&builder, &out.program);
   RenameReservedKeywords(&ctx, kReservedKeywords);
   ctx.Clone();
-  return Output{Program(std::move(out))};
+  return Output{Program(std::move(builder))};
 }
 
 }  // namespace transform
diff --git a/src/writer/hlsl/test_helper.h b/src/writer/hlsl/test_helper.h
index 2f5f356344..de6611c362 100644
--- a/src/writer/hlsl/test_helper.h
+++ b/src/writer/hlsl/test_helper.h
@@ -20,9 +20,7 @@
 #include <utility>
 
 #include "gtest/gtest.h"
-#include "src/transform/canonicalize_entry_point_io.h"
 #include "src/transform/hlsl.h"
-#include "src/transform/manager.h"
 #include "src/writer/hlsl/generator_impl.h"
 
 namespace tint {
@@ -101,11 +99,7 @@ class TestHelperBase : public BODY, public ProgramBuilder {
           << formatter.format(program->Diagnostics());
     }();
 
-    tint::transform::Manager transform_manager;
-    transform_manager.append(
-        std::make_unique<tint::transform::CanonicalizeEntryPointIO>());
-    transform_manager.append(std::make_unique<tint::transform::Hlsl>());
-    auto result = transform_manager.Run(program.get());
+    auto result = transform::Hlsl().Run(program.get());
     [&]() {
       ASSERT_TRUE(result.program.IsValid())
           << formatter.format(result.program.Diagnostics());
diff --git a/src/writer/msl/test_helper.h b/src/writer/msl/test_helper.h
index a40d2c3bcf..37d5200e87 100644
--- a/src/writer/msl/test_helper.h
+++ b/src/writer/msl/test_helper.h
@@ -20,8 +20,6 @@
 
 #include "gtest/gtest.h"
 #include "src/program_builder.h"
-#include "src/transform/canonicalize_entry_point_io.h"
-#include "src/transform/manager.h"
 #include "src/transform/msl.h"
 #include "src/writer/msl/generator_impl.h"
 
@@ -76,11 +74,7 @@ class TestHelperBase : public BASE, public ProgramBuilder {
           << diag::Formatter().format(program->Diagnostics());
     }();
 
-    tint::transform::Manager transform_manager;
-    transform_manager.append(
-        std::make_unique<tint::transform::CanonicalizeEntryPointIO>());
-    transform_manager.append(std::make_unique<tint::transform::Msl>());
-    auto result = transform_manager.Run(program.get());
+    auto result = transform::Msl().Run(program.get());
     [&]() {
       ASSERT_TRUE(result.program.IsValid())
           << diag::Formatter().format(result.program.Diagnostics());