diff --git a/deployments/crypto/crypto.cmake b/deployments/crypto/crypto.cmake
index 64c3b1c..3f3df3c 100644
--- a/deployments/crypto/crypto.cmake
+++ b/deployments/crypto/crypto.cmake
@@ -62,15 +62,18 @@
 
 # Get libc include dir
 get_property(LIBC_INCLUDE_PATH TARGET stdlib::c PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+get_property(LIBC_SYSTEM_INCLUDE_PATH TARGET stdlib::c PROPERTY INTERFACE_SYSTEM_INCLUDE_DIRECTORIES)
 
 # Nanopb
 list(APPEND NANOPB_EXTERNAL_INCLUDE_PATHS ${LIBC_INCLUDE_PATH})
+list(APPEND NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS ${LIBC_SYSTEM_INCLUDE_PATH})
 include(../../../external/nanopb/nanopb.cmake)
 target_link_libraries(crypto PRIVATE nanopb::protobuf-nanopb-static)
 protobuf_generate_all(TGT "crypto" NAMESPACE "protobuf" BASE_DIR "${TS_ROOT}/protocols")
 
 # Mbed TLS provides libmbedcrypto
 list(APPEND MBEDTLS_EXTRA_INCLUDES ${LIBC_INCLUDE_PATH})
+list(APPEND MBEDTLS_EXTERNAL_SYSTEM_INCLUDE_PATHS ${LIBC_SYSTEM_INCLUDE_PATH})
 include(../../../external/MbedTLS/MbedTLS.cmake)
 target_link_libraries(crypto PRIVATE mbedcrypto)
 target_link_libraries(mbedcrypto INTERFACE stdlib::c)
diff --git a/deployments/se-proxy/se-proxy.cmake b/deployments/se-proxy/se-proxy.cmake
index 180286d..1083717 100644
--- a/deployments/se-proxy/se-proxy.cmake
+++ b/deployments/se-proxy/se-proxy.cmake
@@ -69,10 +69,12 @@
 #-------------------------------------------------------------------------------
 
 # Get libc include dir
-get_property(LIBC_INCLUDE_PATH TARGET c PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+get_property(LIBC_INCLUDE_PATH TARGET stdlib::c PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+get_property(LIBC_SYSTEM_INCLUDE_PATH TARGET stdlib::c PROPERTY INTERFACE_SYSTEM_INCLUDE_DIRECTORIES)
 
 # Nanopb
 list(APPEND NANOPB_EXTERNAL_INCLUDE_PATHS ${LIBC_INCLUDE_PATH})
+list(APPEND NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS ${LIBC_SYSTEM_INCLUDE_PATH})
 include(../../../external/nanopb/nanopb.cmake)
 target_link_libraries(se-proxy PRIVATE nanopb::protobuf-nanopb-static)
 protobuf_generate_all(TGT "se-proxy" NAMESPACE "protobuf" BASE_DIR "${TS_ROOT}/protocols")
diff --git a/external/nanopb/nanopb-init-cache.cmake.in b/external/nanopb/nanopb-init-cache.cmake.in
index 3f34ca9..c361812 100644
--- a/external/nanopb/nanopb-init-cache.cmake.in
+++ b/external/nanopb/nanopb-init-cache.cmake.in
@@ -20,7 +20,16 @@
 endif()
 
 set(NANOPB_EXTERNAL_INCLUDE_PATHS "@NANOPB_EXTERNAL_INCLUDE_PATHS@" CACHE STRING "")
+set(NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS "@NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS@" CACHE STRING "")
 
 if (NOT "${NANOPB_EXTERNAL_INCLUDE_PATHS}" STREQUAL "")
-	include_directories(${NANOPB_EXTERNAL_INCLUDE_PATHS})
+	string(REPLACE " " " -I " NANOPB_EXTERNAL_INCLUDE_PATHS "${NANOPB_EXTERNAL_INCLUDE_PATHS}")
+	string(APPEND CMAKE_C_FLAGS_INIT " -I ${NANOPB_EXTERNAL_INCLUDE_PATHS}")
 endif()
+
+if (NOT "${NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS}" STREQUAL "")
+	string(REPLACE " " " -isystem " NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS "${NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS}")
+	string(APPEND CMAKE_C_FLAGS_INIT " -isystem ${NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS}")
+endif()
+
+set(CMAKE_C_FLAGS_INIT "${CMAKE_C_FLAGS_INIT}" CACHE STRING "")
diff --git a/external/nanopb/nanopb.cmake b/external/nanopb/nanopb.cmake
index c805829..3777fa3 100644
--- a/external/nanopb/nanopb.cmake
+++ b/external/nanopb/nanopb.cmake
@@ -50,9 +50,12 @@
 		COMMAND git apply ${CMAKE_CURRENT_LIST_DIR}/fix-pyhon-name.patch
   )
 
-if (NOT "${NANOPB_EXTERNAL_INCLUDE_PATHS}" STREQUAL "")
-	string(REPLACE ";" " " NANOPB_EXTERNAL_INCLUDE_PATHS "${NANOPB_EXTERNAL_INCLUDE_PATHS}")
-endif()
+# Convert include path list to string
+foreach(_var IN ITEMS NANOPB_EXTERNAL_INCLUDE_PATHS NANOPB_EXTERNAL_SYSTEM_INCLUDE_PATHS)
+	if (NOT "${${_var}}" STREQUAL "")
+		string(REPLACE ";" " " ${_var} "${${_var}}")
+	endif()
+endforeach()
 
 include(${TS_ROOT}/tools/cmake/common/LazyFetch.cmake REQUIRED)
 LazyFetch_MakeAvailable(DEP_NAME nanopb