diff --git a/xls/contrib/mlir/BUILD b/xls/contrib/mlir/BUILD
index a420bc2d0c..989b126142 100644
--- a/xls/contrib/mlir/BUILD
+++ b/xls/contrib/mlir/BUILD
@@ -367,11 +367,13 @@ cc_library(
         ":xls_transforms_passes",
         ":xls_transforms_passes_inc_gen",
         ":xls_translate_lib",
+        "//xls/ir:clone_package",
         "//xls/passes:pass_pipeline_cc_proto",
         "//xls/tools:opt",
         "@com_google_absl//absl/status",
         "@com_google_protobuf//:protobuf",
         "@llvm-project//llvm:Support",
+        "@llvm-project//mlir:FuncDialect",
         "@llvm-project//mlir:IR",
         "@llvm-project//mlir:Pass",
         "@llvm-project//mlir:Support",
diff --git a/xls/contrib/mlir/transforms/optimize_using_xls.cc b/xls/contrib/mlir/transforms/optimize_using_xls.cc
index a97f68fa90..09b37eba72 100644
--- a/xls/contrib/mlir/transforms/optimize_using_xls.cc
+++ b/xls/contrib/mlir/transforms/optimize_using_xls.cc
@@ -12,12 +12,15 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
+#include <cstddef>
 #include <memory>
 #include <optional>
 #include <string>
+#include <utility>
 
 #include "absl/status/status.h"
 #include "llvm/include/llvm/Support/DebugLog.h"
+#include "mlir/include/mlir/Dialect/Func/IR/FuncOps.h"
 #include "mlir/include/mlir/IR/BuiltinOps.h"
 #include "mlir/include/mlir/IR/Diagnostics.h"
 #include "mlir/include/mlir/IR/MLIRContext.h"
@@ -29,6 +32,7 @@
 #include "xls/contrib/mlir/tools/xls_translate/xls_translate_from_mlir.h"
 #include "xls/contrib/mlir/tools/xls_translate/xls_translate_to_mlir.h"
 #include "xls/contrib/mlir/transforms/passes.h"  // IWYU pragma: keep
+#include "xls/ir/clone_package.h"
 #include "xls/passes/pass_pipeline.pb.h"
 #include "xls/tools/opt.h"
 
@@ -64,16 +68,15 @@ void OptimizeUsingXlsPass::runOnOperation() {
 }
 
 LogicalResult optimizeUsingXls(ModuleOp module, DslxPackageCache& dslx_cache,
-                               std::optional<std::string> xls_pipeline) {
+                               std::optional<std::string> xls_pipeline,
+                               ArrayRef<StringRef> tops) {
   FailureOr<std::unique_ptr<::xls::Package>> package =
-      mlirXlsToXls(module,
-                   /*dslx_search_path=*/"", dslx_cache);
+      mlirXlsToXls(module, /*dslx_search_path=*/"", dslx_cache);
   if (failed(package)) {
     return failure();
   }
 
   ::xls::tools::OptOptions opt_options;
-  opt_options.top = module.getName().value_or("_package");
   if (xls_pipeline.has_value()) {
     ::xls::PassPipelineProto pass_pipeline;
     if (!google::protobuf::TextFormat::ParseFromString(*xls_pipeline, &pass_pipeline)) {
@@ -83,25 +86,80 @@ LogicalResult optimizeUsingXls(ModuleOp module, DslxPackageCache& dslx_cache,
     opt_options.pass_pipeline = pass_pipeline;
   }
 
-  if (!xls_pipeline.has_value() || !xls_pipeline->empty()) {
-    LDBG() << "Optimizing IR for top: '" << opt_options.top << "using \n\t"
-           << xls_pipeline.value_or("default pipeline");
+  bool is_empty_tops = tops.empty();
+  std::string default_top;
+  SmallVector<StringRef> actual_tops(tops.begin(), tops.end());
 
-    absl::Status status =
-        ::xls::tools::OptimizeIrForTop(package->get(), opt_options);
-    if (!status.ok()) {
-      return module.emitError("failed to optimize IR: ") << status.ToString();
-    }
+  if (is_empty_tops) {
+    default_top = module.getName().value_or("_package").str();
+    actual_tops.push_back(default_top);
   }
 
-  OwningOpRef<Operation*> new_module_op =
-      XlsToMlirXlsTranslate(**package, module.getContext());
-  if (!new_module_op) {
-    return module.emitError(
-        "failed to translate optimized XLS IR back to MLIR");
+  for (size_t i = 0; i < actual_tops.size(); ++i) {
+    StringRef top = actual_tops[i];
+    bool is_last = (i == actual_tops.size() - 1);
+
+    ::xls::Package* pkg_to_optimize;
+    std::unique_ptr<::xls::Package> pkg_clone;
+
+    if (is_last) {
+      // For the last (or only) top, we don't need to clone. We can just mutate
+      // the original package directly.
+      pkg_to_optimize = package->get();
+    } else {
+      auto pkg_clone_or = ::xls::ClonePackage((*package).get());
+      if (!pkg_clone_or.ok()) {
+        return module.emitError("failed to clone package: ")
+               << pkg_clone_or.status().ToString();
+      }
+      pkg_clone = std::move(pkg_clone_or).value();
+      pkg_to_optimize = pkg_clone.get();
+    }
+
+    opt_options.top = top.str();
+
+    if (!xls_pipeline.has_value() || !xls_pipeline->empty()) {
+      LDBG() << "Optimizing IR for top: '" << opt_options.top << "' using \n\t"
+             << xls_pipeline.value_or("default pipeline");
+
+      absl::Status status =
+          ::xls::tools::OptimizeIrForTop(pkg_to_optimize, opt_options);
+      if (!status.ok()) {
+        return module.emitError("failed to optimize IR: ") << status.ToString();
+      }
+    }
+
+    OwningOpRef<Operation*> new_module_op =
+        XlsToMlirXlsTranslate(*pkg_to_optimize, module.getContext());
+    if (!new_module_op) {
+      return module.emitError(
+          "failed to translate optimized XLS IR back to MLIR");
+    }
+
+    if (is_empty_tops) {
+      // If no explicit tops were given, preserve the original
+      // behavior of replacing the entire module body.
+      module.getBodyRegion().takeBody(
+          cast<ModuleOp>(*new_module_op).getBodyRegion());
+    } else {
+      // Merge the optimized top function back into the module.
+      // NOTE: This assumes XLS optimization preserves the function signature.
+      // If the function type were to change, we would also need to update all
+      // call sites in the module to avoid producing invalid IR.
+      ModuleOp new_module = cast<ModuleOp>(*new_module_op);
+      auto optimized_func = new_module.lookupSymbol<mlir::func::FuncOp>(top);
+      if (!optimized_func) {
+        return module.emitError("could not find optimized func ") << top;
+      }
+      auto original_func = module.lookupSymbol<mlir::func::FuncOp>(top);
+      if (!original_func) {
+        return module.emitError("could not find original func ") << top;
+      }
+      original_func.setType(optimized_func.getFunctionType());
+      original_func.getBody().takeBody(optimized_func.getBody());
+    }
   }
-  module.getBodyRegion().takeBody(
-      cast<ModuleOp>(*new_module_op).getBodyRegion());
+
   return success();
 }
 
diff --git a/xls/contrib/mlir/transforms/passes.h b/xls/contrib/mlir/transforms/passes.h
index ecf76b6747..397a7b2952 100644
--- a/xls/contrib/mlir/transforms/passes.h
+++ b/xls/contrib/mlir/transforms/passes.h
@@ -35,10 +35,14 @@ class DslxPackageCache;
 #define GEN_PASS_REGISTRATION
 #include "xls/contrib/mlir/transforms/passes.h.inc"  // IWYU pragma: export
 
-// Optimizes the given MLIR module using XLS.
+// Optimizes the given MLIR module using XLS. When tops is empty (default),
+// the module name is used as the single top and the entire module body is
+// replaced. When tops is non-empty, only the specified functions are optimized
+// and spliced back into the module.
 LogicalResult optimizeUsingXls(
     ModuleOp module, DslxPackageCache& dslx_cache,
-    std::optional<std::string> xls_pipeline = std::nullopt);
+    std::optional<std::string> xls_pipeline = std::nullopt,
+    ArrayRef<StringRef> tops = {});
 
 }  // namespace mlir::xls