diff --git a/esphome/core/__init__.py b/esphome/core/__init__.py
index a4fd2ced30..2ec2a08e83 100644
--- a/esphome/core/__init__.py
+++ b/esphome/core/__init__.py
@@ -992,7 +992,8 @@ class EsphomeCore:
     @property
     def using_native_toolchain(self):
         """Whether the selected toolchain builds natively, without reading
-        ``platformio.ini`` (see ``NATIVE_TOOLCHAINS`` in ``esphome.const``)."""
+        ``platformio.ini`` (see ``NATIVE_TOOLCHAINS`` in ``esphome.const``;
+        keep its membership in sync with ``write_cpp_file``'s dispatch)."""
         return self.toolchain in NATIVE_TOOLCHAINS
 
     @property
diff --git a/esphome/core/config.py b/esphome/core/config.py
index 34d5f8c67f..3d57c5af1d 100644
--- a/esphome/core/config.py
+++ b/esphome/core/config.py
@@ -596,9 +596,11 @@ async def _add_platformio_options(pio_options: dict[str, str | list[str]]) -> No
                 # discovered dependencies
                 cg.add_platformio_option(key, vals)
             elif key in NATIVE_ARDUINO_PIO_OPTIONS and CORE.using_toolchain_arduino:
-                # The esp8266 native generator reads these; other native
+                # The esp8266 native generator reads these as scalars; the
+                # schema also permits the list form, where the last value
+                # wins like a later platformio.ini line. Other native
                 # toolchains have no equivalent and fall through to the warning.
-                cg.add_platformio_option(key, val)
+                cg.add_platformio_option(key, vals[-1])
             elif key != "upload_speed":
                 # upload_speed needs no handling: it is read from the raw
                 # config at upload time (upload_using_esptool)
diff --git a/tests/unit_tests/core/test_config.py b/tests/unit_tests/core/test_config.py
index 53ed85dacb..1e632d9628 100644
--- a/tests/unit_tests/core/test_config.py
+++ b/tests/unit_tests/core/test_config.py
@@ -1408,7 +1408,9 @@ async def test_add_platformio_options_native_arduino(
     await config._add_platformio_options(
         {
             "board_build.f_cpu": "160000000L",
-            "board_build.ldscript": "eagle.flash.4m2m.ld",
+            # The schema also permits the list form; the last value wins
+            # and reaches the generator as a scalar
+            "board_build.ldscript": ["eagle.flash.2m.ld", "eagle.flash.4m2m.ld"],
             "board_build.filesystem": "littlefs",
             "upload_speed": "115200",
         }