diff --git a/Kconfig.zephyr b/Kconfig.zephyr
index 920da3f410f..7391d570766 100644
--- a/Kconfig.zephyr
+++ b/Kconfig.zephyr
@@ -460,17 +460,6 @@ config NATIVE_BUILD
 	  Zephyr will be built targeting the host system for debug and
 	  development purposes.
 
-config NATIVE_APPLICATION
-	bool
-	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. This option is deprecated
-	  and will be removed in Zephyr v4.3
-
 config NATIVE_LIBRARY
 	bool
 	select NATIVE_BUILD
diff --git a/lib/cpp/Kconfig b/lib/cpp/Kconfig
index da309ee3fbc..acd4fe50c23 100644
--- a/lib/cpp/Kconfig
+++ b/lib/cpp/Kconfig
@@ -111,7 +111,6 @@ config MINIMAL_LIBCPP
 
 config GLIBCXX_LIBCPP
 	bool "GNU C++ Standard Library"
-	depends on !NATIVE_APPLICATION
 	depends on NEWLIB_LIBC || PICOLIBC
 	select FULL_LIBCPP_SUPPORTED
 	help
@@ -120,7 +119,6 @@ config GLIBCXX_LIBCPP
 
 config LIBCXX_LIBCPP
 	bool "LLVM C++ Standard Library"
-	depends on !NATIVE_APPLICATION
 	depends on NEWLIB_LIBC
 	depends on "$(ZEPHYR_TOOLCHAIN_VARIANT)" = "llvm"
 	select FULL_LIBCPP_SUPPORTED
@@ -131,7 +129,6 @@ config LIBCXX_LIBCPP
 
 config ARCMWDT_LIBCPP
 	bool "ARC MWDT C++ Library"
-	depends on !NATIVE_APPLICATION
 	depends on ARCMWDT_LIBC
 	help
 	  Build with ARC MetaWare C++ Standard Library provided by the ARC
diff --git a/lib/libc/Kconfig b/lib/libc/Kconfig
index ff7309965e5..06eb5990237 100644
--- a/lib/libc/Kconfig
+++ b/lib/libc/Kconfig
@@ -27,7 +27,6 @@ config FULL_LIBC_SUPPORTED
 
 config MINIMAL_LIBC_SUPPORTED
 	bool
-	depends on !NATIVE_APPLICATION
 	default y
 	help
 	  Selected when the target has support for the minimal C library
@@ -36,7 +35,6 @@ config NEWLIB_LIBC_SUPPORTED
 	bool
 	default y
 	depends on "$(TOOLCHAIN_HAS_NEWLIB)" = "y"
-	depends on !NATIVE_APPLICATION
 	select FULL_LIBC_SUPPORTED
 	help
 	  Selected when the target has support for the newlib C library
@@ -44,7 +42,6 @@ config NEWLIB_LIBC_SUPPORTED
 # Picolibc with C++ support in Zephyr SDK is handled by Zephyr SDK's own Kconfig.
 config PICOLIBC_SUPPORTED
 	bool
-	depends on !NATIVE_APPLICATION
 	depends on ("$(TOOLCHAIN_HAS_PICOLIBC)" = "y") || (ZEPHYR_PICOLIBC_MODULE && !REQUIRES_FULL_LIBCPP)
 	default y
 	select FULL_LIBC_SUPPORTED
@@ -125,7 +122,6 @@ config NEWLIB_LIBC
 
 config ARCMWDT_LIBC
 	bool "ARC MWDT C library"
-	depends on !NATIVE_APPLICATION
 	depends on "$(ZEPHYR_TOOLCHAIN_VARIANT)" = "arcmwdt"
 	select STATIC_INIT_GNU
 	help
@@ -160,7 +156,7 @@ rsource "picolibc/Kconfig"
 config STDOUT_CONSOLE
 	bool "Send stdout to console"
 	depends on CONSOLE_HAS_DRIVER
-	depends on !(NATIVE_APPLICATION || (NATIVE_LIBRARY && EXTERNAL_LIBC))
+	depends on !(NATIVE_LIBRARY && EXTERNAL_LIBC)
 	default y
 	help
 	  This option directs standard output (e.g. printf) to the console
diff --git a/lib/posix/options/Kconfig.compat b/lib/posix/options/Kconfig.compat
index a07c2b12579..e15cc869a7b 100644
--- a/lib/posix/options/Kconfig.compat
+++ b/lib/posix/options/Kconfig.compat
@@ -7,7 +7,6 @@ menu "Miscellaneous POSIX-related options"
 
 config EVENTFD
 	bool "Support for eventfd"
-	depends on !NATIVE_APPLICATION
 	select ZVFS
 	select ZVFS_EVENTFD
 	help
diff --git a/lib/posix/options/Kconfig.profile b/lib/posix/options/Kconfig.profile
index b14a7d7c825..99dc78c20ea 100644
--- a/lib/posix/options/Kconfig.profile
+++ b/lib/posix/options/Kconfig.profile
@@ -4,14 +4,12 @@
 
 config POSIX_SYSTEM_HEADERS
 	bool
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	help
 	  Make POSIX headers available to the system without the "zephyr/posix" prefix.
 
 config POSIX_API
 	bool "POSIX APIs"
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	select POSIX_SYSTEM_HEADERS
 	select POSIX_BASE_DEFINITIONS # clock_gettime(), pthread_create(), sem_get(), etc
@@ -46,7 +44,6 @@ config POSIX_AEP_CHOICE_NONE
 
 config POSIX_AEP_CHOICE_BASE
 	bool "Base definitions (system interfaces)"
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	select POSIX_BASE_DEFINITIONS
 	help
@@ -57,7 +54,6 @@ config POSIX_AEP_CHOICE_BASE
 
 config POSIX_AEP_CHOICE_PSE51
 	bool "Minimal Realtime System Profile (PSE51)"
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	select POSIX_BASE_DEFINITIONS
 	select POSIX_AEP_REALTIME_MINIMAL
@@ -71,7 +67,6 @@ config POSIX_AEP_CHOICE_PSE51
 
 config POSIX_AEP_CHOICE_PSE52
 	bool "Realtime Controller System Profile (PSE52)"
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	select POSIX_BASE_DEFINITIONS
 	select POSIX_AEP_REALTIME_MINIMAL
@@ -86,7 +81,6 @@ config POSIX_AEP_CHOICE_PSE52
 
 config POSIX_AEP_CHOICE_PSE53
 	bool "Dedicated Realtime System Profile (PSE53)"
-	depends on !NATIVE_APPLICATION
 	select NATIVE_LIBC_INCOMPATIBLE
 	select POSIX_BASE_DEFINITIONS
 	select POSIX_AEP_REALTIME_MINIMAL