diff --git a/configure.ac b/configure.ac
index 3c838b92..91708583 100644
--- a/configure.ac
+++ b/configure.ac
@@ -181,7 +181,7 @@ LIBTOOL_EXTRA_FLAGS="$LIBTOOL_EXTRA_FLAGS -version-info $SODIUM_LIBRARY_VERSION"
 AC_ARG_ENABLE(soname-versions,
   [AC_HELP_STRING([--enable-soname-versions], [enable soname versions (must be disabled for Android) (default: enabled)])],
     [
-	AS_IF([test "x$enableval" = "xno"], [
+        AS_IF([test "x$enableval" = "xno"], [
           LIBTOOL_EXTRA_FLAGS="$LIBTOOL_OLD_FLAGS -avoid-version"
         ])
     ]
@@ -263,19 +263,21 @@ dnl Checks for headers
 AS_IF([test "x$EMSCRIPTEN" = "x"],[
 
   AC_MSG_CHECKING(for MMX instructions set)
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-mmmx], [CFLAGS="$CFLAGS -mmmx"])
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("mmx")
-#ifndef __MMX__
-# define __MMX__
-#endif
 #include <mmintrin.h>
 ]], [[ __m64 x = _mm_setzero_si64(); ]])],
     [AC_MSG_RESULT(yes)
      AC_DEFINE([HAVE_MMINTRIN_H], [1], [mmx is available])
      AX_CHECK_COMPILE_FLAG([-mmmx], [CFLAGS_MMX="-mmmx"])],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
 
   AC_MSG_CHECKING(for SSE2 instructions set)
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-msse2], [CFLAGS="$CFLAGS -msse2"])
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("sse2")
 #ifndef __SSE2__
@@ -287,13 +289,13 @@ AS_IF([test "x$EMSCRIPTEN" = "x"],[
      AC_DEFINE([HAVE_EMMINTRIN_H], [1], [sse2 is available])
      AX_CHECK_COMPILE_FLAG([-msse2], [CFLAGS_SSE2="-msse2"])],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
 
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-msse3], [CFLAGS="$CFLAGS -msse3"])
   AC_MSG_CHECKING(for SSE3 instructions set)
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("sse3")
-#ifndef __SSE3__
-# define __SSE3__
-#endif
 #include <pmmintrin.h>
 ]], [[ __m128 x = _mm_addsub_ps(_mm_cvtpd_ps(_mm_setzero_pd()),
                                 _mm_cvtpd_ps(_mm_setzero_pd())); ]])],
@@ -301,43 +303,41 @@ AS_IF([test "x$EMSCRIPTEN" = "x"],[
      AC_DEFINE([HAVE_PMMINTRIN_H], [1], [sse3 is available])
      AX_CHECK_COMPILE_FLAG([-msse3], [CFLAGS_SSE3="-msse3"])],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
 
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-mssse3], [CFLAGS="$CFLAGS -mssse3"])
   AC_MSG_CHECKING(for SSSE3 instructions set)
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("ssse3")
-#ifndef __SSSE3__
-# define __SSSE3__
-#endif
 #include <tmmintrin.h>
 ]], [[ __m64 x = _mm_abs_pi32(_m_from_int(0)); ]])],
     [AC_MSG_RESULT(yes)
      AC_DEFINE([HAVE_TMMINTRIN_H], [1], [ssse3 is available])
      AX_CHECK_COMPILE_FLAG([-mssse3], [CFLAGS_SSSE3="-mssse3"])],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
 
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-msse4.1], [CFLAGS="$CFLAGS -msse4.1"])
   AC_MSG_CHECKING(for SSE4.1 instructions set)
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("sse4.1")
-#ifndef __SSE4_1__
-# define __SSE4_1__
-#endif
 #include <smmintrin.h>
 ]], [[ __m128i x = _mm_minpos_epu16(_mm_setzero_si128()); ]])],
     [AC_MSG_RESULT(yes)
      AC_DEFINE([HAVE_SMMINTRIN_H], [1], [sse4.1 is available])
      AX_CHECK_COMPILE_FLAG([-msse4.1], [CFLAGS_SSE4_1="-msse4.1"])],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
 
+  oldcflags="$CFLAGS"
+  AX_CHECK_COMPILE_FLAG([-maes], [CFLAGS="$CFLAGS -maes"])
+  AX_CHECK_COMPILE_FLAG([-mpclmul], [CFLAGS="$CFLAGS -mpclmul"])
   AC_MSG_CHECKING(for AESNI instructions set and PCLMULQDQ)
   AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
 #pragma GCC target("aes")
 #pragma GCC target("pclmul")
-#ifndef __AES__
-# define __AES__
-#endif
-#ifndef __PCLMUL__
-# define __PCLMUL__
-#endif
 #include <wmmintrin.h>
 ]], [[ __m128i x = _mm_aesimc_si128(_mm_setzero_si128());
        __m128i y = _mm_clmulepi64_si128(_mm_setzero_si128(), _mm_setzero_si128(), 0);]])],
@@ -347,6 +347,8 @@ AS_IF([test "x$EMSCRIPTEN" = "x"],[
      AX_CHECK_COMPILE_FLAG([-mpclmul], [CFLAGS_PCLMUL="-mpclmul"])
      ],
     [AC_MSG_RESULT(no)])
+  CFLAGS="$oldcflags"
+
 ])
 
 AC_SUBST(CFLAGS_MMX)