diff --git a/src/clone_context.cc b/src/clone_context.cc
index 587e593805..902366086a 100644
--- a/src/clone_context.cc
+++ b/src/clone_context.cc
@@ -26,8 +26,18 @@ namespace tint {
 CloneContext::ListTransforms::ListTransforms() = default;
 CloneContext::ListTransforms::~ListTransforms() = default;
 
-CloneContext::CloneContext(ProgramBuilder* to, Program const* from)
-    : dst(to), src(from) {}
+CloneContext::CloneContext(ProgramBuilder* to,
+                           Program const* from,
+                           bool auto_clone_symbols)
+    : dst(to), src(from) {
+  if (auto_clone_symbols) {
+    // Almost all transforms will want to clone all symbols before doing any
+    // work, to avoid any newly created symbols clashing with existing symbols
+    // in the source program and causing them to be renamed.
+    from->Symbols().Foreach([&](Symbol s, const std::string&) { Clone(s); });
+  }
+}
+
 CloneContext::~CloneContext() = default;
 
 Symbol CloneContext::Clone(Symbol s) {
@@ -39,11 +49,6 @@ Symbol CloneContext::Clone(Symbol s) {
   });
 }
 
-CloneContext& CloneContext::CloneSymbols() {
-  src->Symbols().Foreach([&](Symbol s, const std::string&) { Clone(s); });
-  return *this;
-}
-
 void CloneContext::Clone() {
   dst->AST().Copy(this, &src->AST());
 }
diff --git a/src/clone_context.h b/src/clone_context.h
index 1243e342c7..2ff66caaac 100644
--- a/src/clone_context.h
+++ b/src/clone_context.h
@@ -63,7 +63,10 @@ class CloneContext {
   /// Constructor
   /// @param to the target ProgramBuilder to clone into
   /// @param from the source Program to clone from
-  CloneContext(ProgramBuilder* to, Program const* from);
+  /// @param auto_clone_symbols clone all symbols in `from` before returning
+  CloneContext(ProgramBuilder* to,
+               Program const* from,
+               bool auto_clone_symbols = true);
 
   /// Destructor
   ~CloneContext();
@@ -150,12 +153,6 @@ class CloneContext {
   /// @return the cloned source
   Symbol Clone(Symbol s);
 
-  /// Clones all the Symbols in `src->Symbols()` into #dst.
-  /// This may be used to ensure that authored symbols are not suffixed with a
-  /// unique identifier if they collide with other symbols.
-  /// @returns this CloneContext so calls can be chained
-  CloneContext& CloneSymbols();
-
   /// Clones each of the elements of the vector `v` into the ProgramBuilder
   /// #dst.
   ///
diff --git a/src/clone_context_test.cc b/src/clone_context_test.cc
index ea6f90242e..c64ca9f5ae 100644
--- a/src/clone_context_test.cc
+++ b/src/clone_context_test.cc
@@ -224,7 +224,7 @@ TEST(CloneContext, CloneWithReplaceAll_Symbols) {
   // N: Node
 
   ProgramBuilder cloned;
-  auto* cloned_root = CloneContext(&cloned, &original)
+  auto* cloned_root = CloneContext(&cloned, &original, false)
                           .ReplaceAll([&](Symbol sym) {
                             auto in = original.Symbols().NameFor(sym);
                             auto out = "transformed<" + in + ">";
@@ -435,7 +435,7 @@ TEST(CloneContext, CloneNewUnnamedSymbols) {
   Program original(std::move(builder));
 
   ProgramBuilder cloned;
-  CloneContext ctx(&cloned, &original);
+  CloneContext ctx(&cloned, &original, false);
   Symbol new_x = cloned.Symbols().New();
   Symbol new_a = ctx.Clone(old_a);
   Symbol new_y = cloned.Symbols().New();
@@ -463,7 +463,7 @@ TEST(CloneContext, CloneNewSymbols) {
   Program original(std::move(builder));
 
   ProgramBuilder cloned;
-  CloneContext ctx(&cloned, &original);
+  CloneContext ctx(&cloned, &original, false);
   Symbol new_x = cloned.Symbols().New("a");
   Symbol new_a = ctx.Clone(old_a);
   Symbol new_y = cloned.Symbols().New("b");
@@ -492,7 +492,6 @@ TEST(CloneContext, CloneNewSymbols_AfterCloneSymbols) {
 
   ProgramBuilder cloned;
   CloneContext ctx(&cloned, &original);
-  ctx.CloneSymbols();
   Symbol new_x = cloned.Symbols().New("a");
   Symbol new_a = ctx.Clone(old_a);
   Symbol new_y = cloned.Symbols().New("b");
diff --git a/src/transform/bound_array_accessors.cc b/src/transform/bound_array_accessors.cc
index 3f6416b42c..e66866d352 100644
--- a/src/transform/bound_array_accessors.cc
+++ b/src/transform/bound_array_accessors.cc
@@ -29,11 +29,6 @@ BoundArrayAccessors::~BoundArrayAccessors() = default;
 Output BoundArrayAccessors::Run(const Program* in, const DataMap&) {
   ProgramBuilder out;
   CloneContext ctx(&out, in);
-
-  // Start by cloning all the symbols. This ensures that the authored symbols
-  // won't get renamed if they collide with new symbols below.
-  ctx.CloneSymbols();
-
   ctx.ReplaceAll([&](ast::ArrayAccessorExpression* expr) {
     return Transform(expr, &ctx);
   });
diff --git a/src/transform/canonicalize_entry_point_io.cc b/src/transform/canonicalize_entry_point_io.cc
index 622b6b2fa4..06bb158bc2 100644
--- a/src/transform/canonicalize_entry_point_io.cc
+++ b/src/transform/canonicalize_entry_point_io.cc
@@ -62,10 +62,6 @@ Output CanonicalizeEntryPointIO::Run(const Program* in, const DataMap&) {
   ProgramBuilder out;
   CloneContext ctx(&out, in);
 
-  // Start by cloning all the symbols. This ensures that the authored symbols
-  // won't get renamed if they collide with new symbols below.
-  ctx.CloneSymbols();
-
   // Strip entry point IO decorations from struct declarations.
   // TODO(jrprice): This code is duplicated with the SPIR-V transform.
   for (auto* ty : ctx.src->AST().ConstructedTypes()) {
diff --git a/src/transform/decompose_storage_access.cc b/src/transform/decompose_storage_access.cc
index d154514663..a5c9e09a16 100644
--- a/src/transform/decompose_storage_access.cc
+++ b/src/transform/decompose_storage_access.cc
@@ -613,10 +613,6 @@ Output DecomposeStorageAccess::Run(const Program* in, const DataMap&) {
   ProgramBuilder out;
   CloneContext ctx(&out, in);
 
-  // Start by cloning all the symbols. This ensures that the authored symbols
-  // won't get renamed if they collide with new symbols below.
-  ctx.CloneSymbols();
-
   auto& sem = ctx.src->Sem();
 
   State state;
diff --git a/src/transform/emit_vertex_point_size.cc b/src/transform/emit_vertex_point_size.cc
index 676d400a3e..048d23a7de 100644
--- a/src/transform/emit_vertex_point_size.cc
+++ b/src/transform/emit_vertex_point_size.cc
@@ -35,10 +35,6 @@ Output EmitVertexPointSize::Run(const Program* in, const DataMap&) {
 
   CloneContext ctx(&out, in);
 
-  // Start by cloning all the symbols. This ensures that the authored symbols
-  // won't get renamed if they collide with new symbols below.
-  ctx.CloneSymbols();
-
   Symbol pointsize = out.Symbols().New("tint_pointsize");
 
   // Declare the pointsize builtin output variable.
diff --git a/src/transform/renamer.cc b/src/transform/renamer.cc
index 9ed474320f..a5a68562ec 100644
--- a/src/transform/renamer.cc
+++ b/src/transform/renamer.cc
@@ -848,7 +848,8 @@ Renamer::~Renamer() = default;
 
 Output Renamer::Run(const Program* in, const DataMap&) {
   ProgramBuilder out;
-  CloneContext ctx(&out, in);
+  // Disable auto-cloning of symbols, since we want to rename them.
+  CloneContext ctx(&out, in, false);
 
   // Swizzles and intrinsic calls need to keep their symbols preserved.
   std::unordered_set<ast::IdentifierExpression*> preserve;
diff --git a/src/transform/vertex_pulling.cc b/src/transform/vertex_pulling.cc
index a34acf37c7..7b5d1a2112 100644
--- a/src/transform/vertex_pulling.cc
+++ b/src/transform/vertex_pulling.cc
@@ -414,10 +414,6 @@ Output VertexPulling::Run(const Program* in, const DataMap& data) {
 
   CloneContext ctx(&out, in);
 
-  // Start by cloning all the symbols. This ensures that the authored symbols
-  // won't get renamed if they collide with new symbols below.
-  ctx.CloneSymbols();
-
   State state{ctx, cfg};
   state.FindOrInsertVertexIndexIfUsed();
   state.FindOrInsertInstanceIndexIfUsed();
diff --git a/src/writer/hlsl/generator_impl_function_test.cc b/src/writer/hlsl/generator_impl_function_test.cc
index cdadf42b8f..c3fa8c43e5 100644
--- a/src/writer/hlsl/generator_impl_function_test.cc
+++ b/src/writer/hlsl/generator_impl_function_test.cc
@@ -126,10 +126,10 @@ struct tint_symbol_2 {
   float value : SV_Target1;
 };
 
-tint_symbol_2 frag_main(tint_symbol_1 tint_symbol_3) {
-  const float foo = tint_symbol_3.foo;
-  const tint_symbol_2 tint_symbol = {foo};
-  return tint_symbol;
+tint_symbol_2 frag_main(tint_symbol_1 tint_symbol) {
+  const float foo = tint_symbol.foo;
+  const tint_symbol_2 tint_symbol_3 = {foo};
+  return tint_symbol_3;
 }
 
 )");
@@ -160,10 +160,10 @@ struct tint_symbol_2 {
   float value : SV_Depth;
 };
 
-tint_symbol_2 frag_main(tint_symbol_1 tint_symbol_3) {
-  const float4 coord = tint_symbol_3.coord;
-  const tint_symbol_2 tint_symbol = {coord.x};
-  return tint_symbol;
+tint_symbol_2 frag_main(tint_symbol_1 tint_symbol) {
+  const float4 coord = tint_symbol.coord;
+  const tint_symbol_2 tint_symbol_3 = {coord.x};
+  return tint_symbol_3;
 }
 
 )");
@@ -210,7 +210,7 @@ TEST_F(HlslGeneratorImplTest_Function,
   float col1;
   float col2;
 };
-struct tint_symbol_1 {
+struct tint_symbol {
   float col1 : TEXCOORD1;
   float col2 : TEXCOORD2;
 };
@@ -219,10 +219,10 @@ struct tint_symbol_3 {
   float col2 : TEXCOORD2;
 };
 
-tint_symbol_1 vert_main() {
-  const Interface tint_symbol_1_1 = {0.5f, 0.25f};
-  const tint_symbol_1 tint_symbol = {tint_symbol_1_1.col1, tint_symbol_1_1.col2};
-  return tint_symbol;
+tint_symbol vert_main() {
+  const Interface tint_symbol_1 = {0.5f, 0.25f};
+  const tint_symbol tint_symbol_4 = {tint_symbol_1.col1, tint_symbol_1.col2};
+  return tint_symbol_4;
 }
 
 void frag_main(tint_symbol_3 tint_symbol_2) {
@@ -278,28 +278,28 @@ TEST_F(HlslGeneratorImplTest_Function,
   EXPECT_EQ(result(), R"(struct VertexOutput {
   float4 pos;
 };
-struct tint_symbol_2 {
+struct tint_symbol {
   float4 pos : SV_Position;
 };
-struct tint_symbol_2_1 {
+struct tint_symbol_2 {
   float4 pos : SV_Position;
 };
 
 VertexOutput foo(float x) {
-  const VertexOutput tint_symbol = {float4(x, x, x, 1.0f)};
-  return tint_symbol;
+  const VertexOutput tint_symbol_4 = {float4(x, x, x, 1.0f)};
+  return tint_symbol_4;
 }
 
-tint_symbol_2 vert_main1() {
-  const VertexOutput tint_symbol_1_1 = {foo(0.5f)};
-  const tint_symbol_2 tint_symbol_1 = {tint_symbol_1_1.pos};
-  return tint_symbol_1;
+tint_symbol vert_main1() {
+  const VertexOutput tint_symbol_1 = {foo(0.5f)};
+  const tint_symbol tint_symbol_5 = {tint_symbol_1.pos};
+  return tint_symbol_5;
 }
 
-tint_symbol_2_1 vert_main2() {
-  const VertexOutput tint_symbol_3_1 = {foo(0.25f)};
-  const tint_symbol_2_1 tint_symbol_3 = {tint_symbol_3_1.pos};
-  return tint_symbol_3;
+tint_symbol_2 vert_main2() {
+  const VertexOutput tint_symbol_3 = {foo(0.25f)};
+  const tint_symbol_2 tint_symbol_6 = {tint_symbol_3.pos};
+  return tint_symbol_6;
 }
 
 )");