diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4a8b080..13d470d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -284,7 +284,8 @@ function(toolchain_deps toolchain_deps_dir toolchain_install_dir toolchain_suffi
         GIT_REPOSITORY https://github.com/Meinersbur/isl
         GIT_TAG isl-${ISL_VERSION}
         DOWNLOAD_DIR ${DOWNLOAD_DIR}
-        CONFIGURE_COMMAND cd <SOURCE_DIR> && ./autogen.sh COMMAND ${compiler_flags} ${wrapper_command} <SOURCE_DIR>/configure
+        CONFIGURE_COMMAND cd <SOURCE_DIR> && ./autogen.sh
+        COMMAND ${CMAKE_COMMAND} -E env ${compiler_flags} ${wrapper_command} <SOURCE_DIR>/configure
         --build=${build_native}
         --host=${toolchain_host}
         --prefix=${toolchain_deps_dir}
@@ -297,7 +298,7 @@ function(toolchain_deps toolchain_deps_dir toolchain_install_dir toolchain_suffi
         URL https://github.com/libexpat/libexpat/releases/download/R_2_3_0/expat-${EXPAT_VERSION}.tar.bz2
         URL_HASH ${EXPAT_HASH}
         DOWNLOAD_DIR ${DOWNLOAD_DIR}
-        CONFIGURE_COMMAND ${compiler_flags} ${wrapper_command} <SOURCE_DIR>/configure
+        CONFIGURE_COMMAND ${CMAKE_COMMAND} -E env ${compiler_flags} ${wrapper_command} <SOURCE_DIR>/configure
         --build=${build_native}
         --host=${toolchain_host}
         --prefix=${toolchain_deps_dir}
@@ -569,7 +570,7 @@ ExternalProject_Add(newlib
     GIT_TAG ${NEWLIB_TAG}
     ${GIT_SHALLOW_SUPPORT}
     # Pass the compiler_target_tools here so newlib picks up the fresh gcc-base compiler
-    CONFIGURE_COMMAND ${compiler_flags} ${toolchain_tools} ${compiler_target_tools}
+    CONFIGURE_COMMAND ${CMAKE_COMMAND} -E env ${compiler_flag} ${toolchain_tools} ${compiler_target_tools}
     ${wrapper_command} <SOURCE_DIR>/configure "CFLAGS_FOR_TARGET=-g -O2 -ffunction-sections -fdata-sections"
     --build=${build_native}
     --host=${host_native}
@@ -583,7 +584,7 @@ ExternalProject_Add(newlib
     --enable-newlib-long-time_t
     --disable-nls
     --enable-newlib-iconv
-    BUILD_COMMAND ${compiler_flags} ${toolchain_tools} ${wrapper_command} $(MAKE)
+    BUILD_COMMAND ${CMAKE_COMMAND} -E env ${compiler_flags} ${toolchain_tools} ${wrapper_command} $(MAKE)
     INSTALL_COMMAND $(MAKE) install DESTDIR=${CMAKE_INSTALL_PREFIX}
     # Install a copy of newlib in the toolchain directory (required for pthread-embedded target)
     COMMAND $(MAKE) install DESTDIR=${toolchain_build_install_dir}
@@ -641,7 +642,7 @@ ExternalProject_Add(pthread-embedded
     # TODO: this project should have a proper makefile to support out-of-source builds
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND ""
-    BUILD_COMMAND ${compiler_flags} ${wrapper_command} $(MAKE)
+    BUILD_COMMAND ${CMAKE_COMMAND} -E env ${compiler_flags} ${wrapper_command} $(MAKE)
     -C <SOURCE_DIR>/platform/vita ${pthread_tools} PREFIX=${CMAKE_INSTALL_PREFIX}
     INSTALL_COMMAND $(MAKE) -C <SOURCE_DIR>/platform/vita PREFIX=${CMAKE_INSTALL_PREFIX}/${target_arch} install
     # Install into the toolchain directory (required for libgomp target)