diff --git a/Kconfig.zephyr b/Kconfig.zephyr
index 77821c359c79f..51ef697f9c530 100644
--- a/Kconfig.zephyr
+++ b/Kconfig.zephyr
@@ -470,9 +470,11 @@ config NATIVE_APPLICATION
 	default y if ARCH_POSIX
 	depends on !NATIVE_LIBRARY
 	select NATIVE_BUILD
+	select DEPRECATED
 	help
 	  Build as a native application that can run on the host and using
-	  resources and libraries provided by the host.
+	  resources and libraries provided by the host. This option is deprecated
+	  and will be removed in Zephyr v4.3
 
 config NATIVE_LIBRARY
 	bool
diff --git a/boards/native/native_sim/Kconfig b/boards/native/native_sim/Kconfig
index c2610e840e784..fc84adda149f9 100644
--- a/boards/native/native_sim/Kconfig
+++ b/boards/native/native_sim/Kconfig
@@ -18,12 +18,13 @@ comment "Native Simular (Single Core) options"
 
 config NATIVE_SIM_NATIVE_POSIX_COMPAT
 	bool "Pretend to be a native_posix board"
-	default y
+	select DEPRECATED
 	help
 	  When this option is set the native_sim board will pretend to be
 	  a native_posix board from kconfig point of view, to allow using it directly with
 	  code which was meant for the native_posix board and checks for the macro
 	  CONFIG_BOARD_NATIVE_POSIX, or requires other kconfig options which depend on it.
+	  This option is deprecated and will be removed in Zephyr v4.3
 
 config NATIVE_SIM_SLOWDOWN_TO_REAL_TIME
 	bool "Slow down execution to real time"
diff --git a/doc/releases/migration-guide-4.1.rst b/doc/releases/migration-guide-4.1.rst
index 8712b6cc9a987..04eabfdcd340d 100644
--- a/doc/releases/migration-guide-4.1.rst
+++ b/doc/releases/migration-guide-4.1.rst
@@ -115,3 +115,12 @@ Modem
 
 Architectures
 *************
+
+* native/POSIX
+
+  * :kconfig:option:`CONFIG_NATIVE_APPLICATION` has been deprecated. Out-of-tree boards using this
+    option should migrate to the native_simulator runner (:github:`81232`).
+    For an example of how this was done with a board in-tree check :github:`61481`.
+  * For the native_sim target :kconfig:option:`CONFIG_NATIVE_SIM_NATIVE_POSIX_COMPAT` has been
+    switched to ``n`` by default, and this option has been deprecated. Ensure your code does not
+    use the :kconfig:option:`CONFIG_BOARD_NATIVE_POSIX` option anymore (:github:`81232`).
diff --git a/doc/releases/release-notes-4.1.rst b/doc/releases/release-notes-4.1.rst
index 40b3dfedfed5a..dff3f100c2c51 100644
--- a/doc/releases/release-notes-4.1.rst
+++ b/doc/releases/release-notes-4.1.rst
@@ -43,6 +43,12 @@ Architectures
 
 * Xtensa
 
+* native/POSIX
+
+  * :kconfig:option:`CONFIG_NATIVE_APPLICATION` has been deprecated.
+  * For the native_sim target :kconfig:option:`CONFIG_NATIVE_SIM_NATIVE_POSIX_COMPAT` has been
+    switched to ``n`` by default, and this option has been deprecated.
+
 Kernel
 ******