diff --git a/build/php.m4 b/build/php.m4
index 012b8753f6f..da316944f3e 100644
--- a/build/php.m4
+++ b/build/php.m4
@@ -128,10 +128,20 @@ AC_DEFUN([PHP_INIT_BUILD_SYSTEM],
 php_shtool=$srcdir/build/shtool
 T_MD=$($php_shtool echo -n -e %B)
 T_ME=$($php_shtool echo -n -e %b)
+
+dnl Create empty Makefile placeholders.
 > Makefile.objects
 > Makefile.fragments
+
+dnl Mark whether the CFLAGS are set to automatic default value by Autoconf, or
+dnl they are manually modified by the environment variable from outside. E.g.
+dnl './configure CFLAGS=...'. Set this before the AC_PROG_CC, where Autoconf
+dnl adjusts the CFLAGS variable, so the checks can modify CFLAGS.
+AS_VAR_IF([CFLAGS],, [auto_cflags=1])
+
 dnl Required programs.
 PHP_PROG_AWK
+
 dnl Run at the end of the configuration, before creating the config.status.
 AC_CONFIG_COMMANDS_PRE(
 [dnl Directory for storing shared objects of extensions.
diff --git a/configure.ac b/configure.ac
index f54b93fdf40..f01cb5379f8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -100,9 +100,6 @@ dnl ----------------------------------------------------------------------------
 
 PHP_INIT_BUILD_SYSTEM
 
-dnl We want this one before the checks, so the checks can modify CFLAGS.
-AS_VAR_IF([CFLAGS],, [auto_cflags=1])
-
 abs_srcdir=`(cd $srcdir; pwd)`
 abs_builddir=`pwd`
 
diff --git a/scripts/phpize.m4 b/scripts/phpize.m4
index 4bfe79dc457..a4d71b0e33c 100644
--- a/scripts/phpize.m4
+++ b/scripts/phpize.m4
@@ -26,7 +26,7 @@ AC_DEFUN([PHP_ALWAYS_SHARED],[
   test "[$]$1" = "no" && $1=yes
 ])dnl
 
-AS_VAR_IF([CFLAGS],, [auto_cflags=1])
+PHP_INIT_BUILD_SYSTEM
 
 abs_srcdir=`(cd $srcdir && pwd)`
 abs_builddir=`pwd`
@@ -65,8 +65,6 @@ PHP_EXECUTABLE=`$PHP_CONFIG --php-binary 2>/dev/null`
 AS_VAR_IF([prefix],,
   [AC_MSG_ERROR([Cannot find php-config. Please use --with-php-config=PATH])])
 
-PHP_INIT_BUILD_SYSTEM
-
 AC_MSG_CHECKING([for PHP prefix])
 AC_MSG_RESULT([$prefix])
 AC_MSG_CHECKING([for PHP includes])