diff --git a/esphome/components/esp32/__init__.py b/esphome/components/esp32/__init__.py
index 2050eb2a88..e2efcff587 100644
--- a/esphome/components/esp32/__init__.py
+++ b/esphome/components/esp32/__init__.py
@@ -1436,7 +1436,7 @@ async def to_code(config):
 
     cg.set_cpp_standard("gnu++20")
     cg.add_build_flag("-DUSE_ESP32")
-    cg.add_build_flag("-DUSE_NATIVE_64BIT_TIME")
+    cg.add_define("USE_NATIVE_64BIT_TIME")
     cg.add_build_flag("-Wl,-z,noexecstack")
     cg.add_define("ESPHOME_BOARD", config[CONF_BOARD])
     variant = config[CONF_VARIANT]
diff --git a/esphome/components/host/__init__.py b/esphome/components/host/__init__.py
index e7876980ec..8adbfb02ec 100644
--- a/esphome/components/host/__init__.py
+++ b/esphome/components/host/__init__.py
@@ -41,7 +41,7 @@ CONFIG_SCHEMA = cv.All(
 
 async def to_code(config):
     cg.add_build_flag("-DUSE_HOST")
-    cg.add_build_flag("-DUSE_NATIVE_64BIT_TIME")
+    cg.add_define("USE_NATIVE_64BIT_TIME")
     cg.add_define("USE_ESPHOME_HOST_MAC_ADDRESS", config[CONF_MAC_ADDRESS].parts)
     cg.add_build_flag("-std=gnu++20")
     cg.add_define("ESPHOME_BOARD", "host")
diff --git a/esphome/components/rp2040/__init__.py b/esphome/components/rp2040/__init__.py
index 4eb5a07752..ea269a47c5 100644
--- a/esphome/components/rp2040/__init__.py
+++ b/esphome/components/rp2040/__init__.py
@@ -169,7 +169,7 @@ async def to_code(config):
     cg.add_platformio_option("lib_compat_mode", "strict")
     cg.add_platformio_option("board", config[CONF_BOARD])
     cg.add_build_flag("-DUSE_RP2040")
-    cg.add_build_flag("-DUSE_NATIVE_64BIT_TIME")
+    cg.add_define("USE_NATIVE_64BIT_TIME")
     cg.set_cpp_standard("gnu++20")
     cg.add_define("ESPHOME_BOARD", config[CONF_BOARD])
     cg.add_define("ESPHOME_VARIANT", "RP2040")
diff --git a/esphome/components/zephyr/__init__.py b/esphome/components/zephyr/__init__.py
index 9cc051af22..4cc71bddca 100644
--- a/esphome/components/zephyr/__init__.py
+++ b/esphome/components/zephyr/__init__.py
@@ -112,7 +112,7 @@ def add_extra_script(stage: str, filename: str, path: Path) -> None:
 
 def zephyr_to_code(config):
     cg.add_build_flag("-DUSE_ZEPHYR")
-    cg.add_build_flag("-DUSE_NATIVE_64BIT_TIME")
+    cg.add_define("USE_NATIVE_64BIT_TIME")
     cg.set_cpp_standard("gnu++20")
     # build is done by west so bypass board checking in platformio
     cg.add_platformio_option("boards_dir", CORE.relative_build_path("boards"))