diff --git a/cmake/modules/NativeExecutable.cmake b/cmake/modules/NativeExecutable.cmake
--- a/cmake/modules/NativeExecutable.cmake
+++ b/cmake/modules/NativeExecutable.cmake
@@ -10,57 +10,86 @@
 	message(FATAL_ERROR "A native build cannot be cross compiled")
 endif()
 
-# If we are cross compiling, create a directory for native build.
-set(NATIVE_BUILD_DIR "${CMAKE_BINARY_DIR}/native")
-set(NATIVE_BINARY_DIR "${NATIVE_BUILD_DIR}/bin")
-set(NATIVE_BUILD_TARGET "${NATIVE_BUILD_DIR}/CMakeCache.txt")
+# It is imperative that NATIVE_BUILD_DIR be in the cache.
+set(NATIVE_BUILD_DIR "${CMAKE_BINARY_DIR}/native" CACHE PATH "The path of the native build directory")
 
-if(NOT __IS_NATIVE_BUILD AND NOT TARGET native-cmake-build)
-	file(MAKE_DIRECTORY ${NATIVE_BUILD_DIR})
-	add_custom_command(
-		OUTPUT ${NATIVE_BUILD_TARGET}
-		COMMAND ${CMAKE_COMMAND}
-			-G "${CMAKE_GENERATOR}"
-			"${CMAKE_SOURCE_DIR}"
-			"-D__IS_NATIVE_BUILD=1"
-			"-DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}"
-			"-DCMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${NATIVE_BINARY_DIR}"
-			# Don't require native third party dependencies we don't need.
-			"-DBUILD_BITCOIN_WALLET=OFF"
-			"-DBUILD_BITCOIN_QT=OFF"
-			"-DBUILD_BITCOIN_ZMQ=OFF"
-			"-DENABLE_QRCODE=OFF"
-			"-DENABLE_UPNP=OFF"
-		WORKING_DIRECTORY ${NATIVE_BUILD_DIR}
-		VERBATIM USES_TERMINAL
-	)
-
-	add_custom_target(native-cmake-build DEPENDS ${NATIVE_BUILD_TARGET})
-endif()
+function(add_native_executable NAME)
+	if(__IS_NATIVE_BUILD)
+		add_executable(${NAME} EXCLUDE_FROM_ALL ${ARGN})
+	else()
+		file(RELATIVE_PATH RELATIVE_PATH "${CMAKE_BINARY_DIR}" "${CMAKE_CURRENT_BINARY_DIR}")
+		set(NATIVE_TARGET "${RELATIVE_PATH}/${NAME}")
+		set(NATIVE_BINARY "${NATIVE_BUILD_DIR}/${NATIVE_TARGET}")
 
-macro(add_native_executable NAME)
-	if(NOT __IS_NATIVE_BUILD)
-		set(NATIVE_BINARY "${NATIVE_BINARY_DIR}/${NAME}")
-		add_custom_target("build-native-${NAME}"
-			COMMAND ${CMAKE_COMMAND}
-				--build "${NATIVE_BUILD_DIR}"
-				--target "${NAME}"
-			DEPENDS ${NATIVE_BUILD_TARGET}
-			BYPRODUCTS ${NATIVE_BINARY}
-			WORKING_DIRECTORY ${NATIVE_BUILD_DIR}
+		# We create a symlink because cmake craps itself if the imported
+		# executable has the same name as the executable itself.
+		# https://cmake.org/pipermail/cmake/2019-May/069480.html
+		add_custom_command(
+			OUTPUT "native-${NAME}"
+			COMMENT "Building native ${NATIVE_TARGET}"
+			COMMAND ${CMAKE_COMMAND} --build "${NATIVE_BUILD_DIR}" --target "${NATIVE_TARGET}"
+			COMMAND ${CMAKE_COMMAND} -E create_symlink "${NATIVE_BINARY}" "native-${NAME}"
+			DEPENDS "${NATIVE_BUILD_DIR}/CMakeCache.txt" ${ARGN}
 			VERBATIM USES_TERMINAL
 		)
 
-		add_executable(${NAME} IMPORTED)
+		add_executable(${NAME} IMPORTED GLOBAL)
+		set_target_properties(${NAME} PROPERTIES IMPORTED_LOCATION "${NATIVE_BINARY}")
+
+		# This obviously cannot depend on a file for some mysterious reasons only
+		# the cmake gods are aware of, so we need a phony custom target.
+		add_custom_target("build-native-${NAME}" DEPENDS "native-${NAME}")
 		add_dependencies(${NAME} "build-native-${NAME}")
-		set_property(TARGET ${NAME} PROPERTY IMPORTED_LOCATION ${NATIVE_BINARY})
-	else()
-		add_executable(${NAME} EXCLUDE_FROM_ALL ${ARGN})
 	endif()
-endmacro(add_native_executable)
+endfunction(add_native_executable)
 
 function(native_target_include_directories)
 	if(__IS_NATIVE_BUILD)
 		target_include_directories(${ARGN})
 	endif()
 endfunction(native_target_include_directories)
+
+function(native_add_cmake_flags)
+	set_property(GLOBAL APPEND PROPERTY _NATIVE_BUILD_CMAKE_FLAGS ${ARGN})
+endfunction(native_add_cmake_flags)
+
+# Internal machinery
+function(_gen_native_cmake_target)
+	message(STATUS "Configuring native build in ${NATIVE_BUILD_DIR}")
+
+	get_property(ARGSLIST GLOBAL PROPERTY _NATIVE_BUILD_CMAKE_FLAGS)
+
+	list(SORT ARGSLIST)
+	list(REMOVE_DUPLICATES ARGSLIST)
+	list(JOIN ARGSLIST " " ARGS)
+
+	file(MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/config")
+	configure_file(
+		"${CMAKE_SOURCE_DIR}/cmake/templates/NativeCmakeRunner.cmake.in"
+		"${CMAKE_BINARY_DIR}/config/run_native_cmake.sh"
+	)
+endfunction(_gen_native_cmake_target)
+
+function(_gen_native_cmake_hook VAR ACCESS)
+	# When CMAKE_CURRENT_LIST_DIR is set to empty, we execute everything.
+	if("${VAR}" STREQUAL "CMAKE_CURRENT_LIST_DIR" AND
+	   "${CMAKE_CURRENT_LIST_DIR}" STREQUAL "" AND
+	   "${ACCESS}" STREQUAL "MODIFIED_ACCESS")
+		_gen_native_cmake_target()
+	endif()
+endfunction(_gen_native_cmake_hook)
+
+if(NOT __IS_NATIVE_BUILD AND NOT TARGET native-cmake-build)
+	# Set a hook to execute when everything is set.
+	variable_watch(CMAKE_CURRENT_LIST_DIR _gen_native_cmake_hook)
+
+	add_custom_command(
+		OUTPUT "${NATIVE_BUILD_DIR}/CMakeCache.txt"
+		COMMAND "${CMAKE_BINARY_DIR}/config/run_native_cmake.sh"
+		DEPENDS "${CMAKE_BINARY_DIR}/config/run_native_cmake.sh"
+		WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
+		VERBATIM USES_TERMINAL
+	)
+
+	add_custom_target(native-cmake-build DEPENDS "${NATIVE_BUILD_DIR}/CMakeCache.txt")
+endif()
diff --git a/cmake/templates/NativeCmakeRunner.cmake.in b/cmake/templates/NativeCmakeRunner.cmake.in
new file mode 100755
--- /dev/null
+++ b/cmake/templates/NativeCmakeRunner.cmake.in
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+mkdir -p "${NATIVE_BUILD_DIR}"
+cd "${NATIVE_BUILD_DIR}"
+${CMAKE_COMMAND} -G${CMAKE_GENERATOR} "${CMAKE_SOURCE_DIR}" \
+    -D__IS_NATIVE_BUILD=1 \
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} \
+    ${ARGS}
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -27,6 +27,16 @@
 option(ENABLE_WERROR "Promote some compiler warnings to errors" OFF)
 option(START_WITH_UPNP "Make UPnP the default to map ports" OFF)
 
+# Disable what we do not need for the native build.
+include(NativeExecutable)
+native_add_cmake_flags(
+	"-DBUILD_BITCOIN_WALLET=OFF"
+	"-DBUILD_BITCOIN_QT=OFF"
+	"-DBUILD_BITCOIN_ZMQ=OFF"
+	"-DENABLE_QRCODE=OFF"
+	"-DENABLE_UPNP=OFF"
+)
+
 # Allow usage of sanitizers by setting ECM_ENABLE_SANITIZERS
 if(ENABLE_SANITIZERS)
 	set(ECM_ENABLE_SANITIZERS ${ENABLE_SANITIZERS})