diff --git a/Makefile b/Makefile
index 6a280ea1b4..bc0056be1a 100644
--- a/Makefile
+++ b/Makefile
@@ -106,6 +106,16 @@ ifneq ($(findstring Win32,$(OS)),)
    LDFLAGS += -mwindows
 endif
 
+ifneq ($(CXX_BUILD), 1)
+   ifneq ($(C89_BUILD),)
+      CFLAGS += -std=c89 -ansi -pedantic -Werror=pedantic -Wno-long-long
+   else ifeq ($(HAVE_C99), 1)
+      CFLAGS += $(C99_CFLAGS)
+   endif
+
+   CFLAGS += -D_GNU_SOURCE
+endif
+
 DEF_FLAGS += -Wall $(INCLUDE_DIRS) -I. -Ideps -Ideps/stb
 
 CFLAGS += $(DEF_FLAGS)
@@ -127,20 +137,6 @@ else
    LINK = $(CC)
 endif
 
-ifneq ($(CXX_BUILD), 1)
-   ifneq ($(GNU90_BUILD), 1)
-      ifneq ($(findstring icc,$(CC)),)
-         CFLAGS += -std=c99 -D_GNU_SOURCE
-      else
-         CFLAGS += -std=gnu99 -D_GNU_SOURCE
-      endif
-   endif
-
-   ifneq ($(C89_BUILD),)
-      CFLAGS += -std=c89 -ansi -pedantic -Werror=pedantic -Wno-long-long
-   endif
-endif
-
 ifeq ($(NOUNUSED), yes)
    CFLAGS += -Wno-unused-result
    CXXFLAGS += -Wno-unused-result
diff --git a/qb/config.libs.sh b/qb/config.libs.sh
index b26065ca0a..19b58bffa4 100644
--- a/qb/config.libs.sh
+++ b/qb/config.libs.sh
@@ -4,7 +4,13 @@
 # Only needed when check_enabled ($2), check_platform, check_lib, check_pkgconf,
 # check_header, check_macro and check_switch are not used.
 
-check_switch '' C99 -std=gnu99 "Cannot find C99 compatible compiler."
+check_switch '' C99 -std=gnu99 ''
+
+if [ "$HAVE_C99" = 'no' ]; then
+   HAVE_C99='auto'
+   check_switch '' C99 -std=c99 'Cannot find a C99 compatible compiler.'
+fi
+
 check_switch cxx CXX11 -std=c++11 ''
 check_switch '' NOUNUSED -Wno-unused-result ''
 add_define MAKEFILE NOUNUSED "$HAVE_NOUNUSED"