diff --git a/eclass/autotools.eclass b/eclass/autotools.eclass
index 9143aa454d0d..1f3289fc9120 100644
--- a/eclass/autotools.eclass
+++ b/eclass/autotools.eclass
@@ -518,6 +518,36 @@ autotools_run_tool() {
 		set -- "${1}" $(autotools_m4dir_include) "${@:2}" $(autotools_m4sysdir_include)
 	fi
 
+	# re-order arguments, bug #680210
+	local _old_args=( ${@} )
+	local _at_command=
+	local _at_file=
+	local -a _at_args=()
+	local _argument=
+
+	for _argument in ${_old_args[*]}; do
+		if [[ -z "${_at_command}" ]]; then
+			_at_command=${_argument}
+			continue
+		fi
+
+		if [[ -z "${_at_file}" && "${_argument}" =~ \.(in|ac)$ ]]; then
+			_at_file=${_argument}
+			continue
+		fi
+
+		_at_args+=( ${_argument} )
+	done
+
+	# make sure file is last argument
+	if [[ -n "${_at_file}" ]]; then
+		_at_args+=( ${_at_file} )
+	fi
+
+	debug-print "\$@ before reordering of arguments: ${@}"
+	set -- "${_at_command}" "${_at_args[@]}"
+	debug-print "\$@ after reordering of arguments: ${@}"
+
 	# If the caller wants to probe something, then let them do it directly.
 	if ${return_output} ; then
 		"$@"
@@ -527,8 +557,19 @@ autotools_run_tool() {
 	printf "***** $1 *****\n***** PWD: ${PWD}\n***** $*\n\n" > "${STDERR_TARGET}"
 
 	ebegin "Running $@"
-	"$@" >> "${STDERR_TARGET}" 2>&1
-	if ! eend $? && ${autofail} ; then
+
+	local _retVal=1
+	if [[ ${WANT_AUTOCONF} = 2.1 && -n "${_at_file}" ]] ; then
+		local _output_file=${_at_file%.*}
+		debug-print "Creating ${PWD}/${_output_file} ..."
+		"$@" > "${_output_file}" 2> "${STDERR_TARGET}"
+		_retVal=$?
+	else
+		"$@" >> "${STDERR_TARGET}" 2>&1
+		_retVal=$?
+	fi
+
+	if ! eend ${_retVal} && ${autofail} ; then
 		echo
 		eerror "Failed Running $1 !"
 		eerror