diff --git a/backends/webgpu/CMakeLists.txt b/backends/webgpu/CMakeLists.txt
index ce108ac8b26..3dface0f712 100644
--- a/backends/webgpu/CMakeLists.txt
+++ b/backends/webgpu/CMakeLists.txt
@@ -62,22 +62,27 @@ target_include_directories(
 
 target_link_libraries(webgpu_backend PRIVATE vulkan_schema executorch_core)
 
-# Native WebGPU backend: Dawn (Tint) + SwiftShader; deps script sets Dawn_DIR.
-# Native-only: browser/Emscripten builds use the system webgpu.h and never reach
-# this find_package (root CMake gates it via EXECUTORCH_BUILD_WEBGPU).
-# dawn::webgpu_dawn's link interface references Threads::Threads.
-find_package(Threads REQUIRED)
-find_package(Dawn REQUIRED)
-set(WEBGPU_GPU_LIB dawn::webgpu_dawn)
-target_link_libraries(webgpu_backend PUBLIC ${WEBGPU_GPU_LIB})
-
-if(APPLE)
-  target_link_libraries(
-    webgpu_backend PRIVATE "-framework Metal" "-framework QuartzCore"
-                           "-framework CoreGraphics" "-framework Foundation"
-  )
+# WASM gets its WebGPU implementation from emdawnwebgpu at executable link time.
+# Native builds link Dawn (Tint) and the platform GPU libraries.
+if(EMSCRIPTEN)
+  target_compile_options(webgpu_backend PUBLIC "--use-port=emdawnwebgpu")
+  # --use-port is also required at link time: the link step pulls in the port's
+  # headers, JS glue, and libraries for consumers that link webgpu_backend.
+  target_link_options(webgpu_backend PUBLIC "--use-port=emdawnwebgpu")
 else()
-  target_link_libraries(webgpu_backend PRIVATE dl m pthread)
+  find_package(Threads REQUIRED)
+  find_package(Dawn REQUIRED)
+  set(WEBGPU_GPU_LIB dawn::webgpu_dawn)
+  target_link_libraries(webgpu_backend PUBLIC ${WEBGPU_GPU_LIB})
+
+  if(APPLE)
+    target_link_libraries(
+      webgpu_backend PRIVATE "-framework Metal" "-framework QuartzCore"
+                             "-framework CoreGraphics" "-framework Foundation"
+    )
+  else()
+    target_link_libraries(webgpu_backend PRIVATE dl m pthread)
+  endif()
 endif()
 
 target_compile_options(webgpu_backend PRIVATE -fexceptions)
diff --git a/backends/webgpu/test/test_cmake_configuration.py b/backends/webgpu/test/test_cmake_configuration.py
new file mode 100644
index 00000000000..f2aafd3ef56
--- /dev/null
+++ b/backends/webgpu/test/test_cmake_configuration.py
@@ -0,0 +1,89 @@
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+# All rights reserved.
+#
+# This source code is licensed under the BSD-style license found in the
+# LICENSE file in the root directory of this source tree.
+
+import pathlib
+import re
+import unittest
+
+
+def _conditional_branches(source: str, condition: str) -> tuple[str, str]:
+    lines = source.splitlines()
+    condition_pattern = re.compile(
+        rf"^\s*if\s*\(\s*{re.escape(condition)}\s*\)\s*$",
+        re.IGNORECASE,
+    )
+    command_pattern = re.compile(r"^\s*([A-Za-z_][A-Za-z0-9_]*)\s*\(")
+    start = next(
+        (index for index, line in enumerate(lines) if condition_pattern.match(line)),
+        None,
+    )
+    if start is None:
+        raise AssertionError(f"if({condition}) branch not found")
+
+    depth = 1
+    else_index = None
+    for index in range(start + 1, len(lines)):
+        match = command_pattern.match(lines[index])
+        if match is None:
+            continue
+        command = match.group(1).lower()
+        if command == "if":
+            depth += 1
+        elif command == "endif":
+            depth -= 1
+            if depth == 0:
+                if else_index is None:
+                    raise AssertionError(f"if({condition}) has no else() branch")
+                return (
+                    "\n".join(lines[start + 1 : else_index]),
+                    "\n".join(lines[else_index + 1 : index]),
+                )
+        elif command == "else" and depth == 1:
+            if else_index is not None:
+                raise AssertionError(f"if({condition}) has multiple else() branches")
+            else_index = index
+    raise AssertionError(f"if({condition}) has no matching endif()")
+
+
+class TestCMakeConfiguration(unittest.TestCase):
+    def test_branch_parser_keeps_nested_conditionals_in_native_branch(self) -> None:
+        source = """
+if ( EMSCRIPTEN )
+  wasm_command()
+else()
+  if(APPLE)
+    apple_command()
+  else()
+    linux_command()
+  endif()
+endif()
+"""
+        wasm_branch, native_branch = _conditional_branches(source, "EMSCRIPTEN")
+
+        self.assertIn("wasm_command()", wasm_branch)
+        self.assertIn("apple_command()", native_branch)
+        self.assertIn("linux_command()", native_branch)
+
+    def test_emscripten_uses_port_instead_of_native_dawn(self) -> None:
+        cmake = pathlib.Path(__file__).parents[1] / "CMakeLists.txt"
+        wasm_branch, native_branch = _conditional_branches(
+            cmake.read_text(), "EMSCRIPTEN"
+        )
+        port_flag = r'"--use-port=emdawnwebgpu"'
+
+        self.assertRegex(
+            wasm_branch,
+            rf"target_compile_options\s*\(\s*webgpu_backend\s+PUBLIC\s+{port_flag}\s*\)",
+        )
+        self.assertRegex(
+            wasm_branch,
+            rf"target_link_options\s*\(\s*webgpu_backend\s+PUBLIC\s+{port_flag}\s*\)",
+        )
+        self.assertNotIn("find_package(Dawn", wasm_branch)
+        self.assertNotIn("--use-port=emdawnwebgpu", native_branch)
+        self.assertRegex(
+            native_branch, r"find_package\s*\(\s*Dawn\s+REQUIRED\s*\)"
+        )