diff --git a/aegisub/Makefile.inc.in b/aegisub/Makefile.inc.in
index a9d262be4..222e37f06 100644
--- a/aegisub/Makefile.inc.in
+++ b/aegisub/Makefile.inc.in
@@ -101,7 +101,6 @@ CFLAGS_PTHREAD     = @PTHREAD_CFLAGS@
 CFLAGS_LIBPULSE    = @LIBPULSE_CFLAGS@
 CFLAGS_UCHARDET    = -I../universalchardet
 
-LDFLAGS_LUA        = @LUA_LDFLAGS@
 LIBS_ALSA          = @ALSA_LIBS@
 LIBS_FFMS2         = @FFMS2_LIBS@
 LIBS_FFTW3         = @FFTW3_LIBS@
@@ -112,10 +111,11 @@ LIBS_HUNSPELL      = @HUNSPELL_LIBS@
 LIBS_ICONV         = @ICONV_LIBS@
 LIBS_LIBASS        = @LIBASS_LIBS@
 LIBS_LIBCURL       = @LIBCURL_LIBS@
+LIBS_LIBPULSE      = @LIBPULSE_LIBS@
+LIBS_LUA           = @LUA_LIBS@
 LIBS_OPENAL        = @OPENAL_LIBS@
 LIBS_PORTAUDIO     = @PORTAUDIO_LIBS@
 LIBS_PTHREAD       = @PTHREAD_LIBS@
-LIBS_LIBPULSE      = @LIBPULSE_LIBS@
 LIBS_UCHARDET     ?= ../universalchardet/libuniversalchardet.a
 
 #####################
diff --git a/aegisub/configure.in b/aegisub/configure.in
index f2b52682a..2bb93ad61 100644
--- a/aegisub/configure.in
+++ b/aegisub/configure.in
@@ -429,20 +429,20 @@ AC_ARG_WITH(lua,
             AS_HELP_STRING([--without-lua],
                            [build without lua 5.1 (auto4)]))
 
-AC_ARG_VAR([LUA_CFLAGS], [CFLAGS to use for LUA 5.1 [autodetect]])
-AC_ARG_VAR([LUA_LDFLAGS], [LDFLAGS to use for LUA 5.1 [autodetect]])
-AC_ARG_VAR([LUA_LIBDIR], [Location of LUA 5.1 library. [none]])
+AS_IF([test x$with_lua = xno], [$with_auto4_lua="no"; lua_disabled="(disabled)"], [
+  # First try pkg-config with several names
+  PKG_CHECK_MODULES(LUA, lua     >= 5.1, [with_auto4_lua="yes"], [
+  PKG_CHECK_MODULES(LUA, lua5.1  >= 5.1, [with_auto4_lua="yes"], [
+  PKG_CHECK_MODULES(LUA, lua-5.1 >= 5.1, [with_auto4_lua="yes"], [
+    # Still not found so try to autodetect
+    AS_IF([test -z "$LUA_CFLAGS"],
+      [AGI_FIND_HEADER([LUA], [lua.hpp],
+                       [/usr/include/lua5.1 /usr/include/lua51 /usr/local/include/lua51 /usr/local/include/lua5.1 /usr/include /usr/local/include])])
 
-AS_IF([test -z "$LUA_CFLAGS"],
-  AGI_FIND_HEADER([LUA], [lua.hpp], [/usr/include/lua5.1 /usr/include/lua51 /usr/local/include/lua51 /usr/local/include/lua5.1 /usr/include /usr/local/include]))
+    AS_IF([test -z "$LUA_LIBS"],
+      [AGI_FIND_LIB([LUA], [lua51 lua-5.1 lua5.1 lua], [])])
 
-AS_IF([test -z "$LUA_LDFLAGS"],
-  AGI_FIND_LIB([LUA], [lua51 lua-5.1 lua5.1 lua], [$LUA_LIBDIR]))
-
-aegisub_save_LIBS="$LIBS"
-LIBS="$LUA_LDFLAGS"
-AS_IF([test x$with_lua = xno], [lua_disabled="(disabled)"], [
-  AC_AGI_COMPILE([Lua 5.1 (auto4)], [lua], [$LUA_CFLAGS], [],[
+    AC_AGI_COMPILE([Lua 5.1 (auto4)], [lua], [$LUA_CFLAGS], [$LUA_LIBS],[
 #include <lua.hpp>
 
 int main () {
@@ -451,15 +451,18 @@ int main () {
   int res = lua_objlen(L, -1) == 4;
   lua_close(L);
   return !res;
-}])])
-LIBS="$aegisub_save_LIBS"
+}])
+    AS_IF([test x$agi_cv_with_lua = xno && test x$with_lua = xyes],
+          [AC_MSG_FAILURE([--with-lua was specified, but lua could not be found. Try setting LUA_CLFAGS and LUA_LIBS manually])])
+    with_auto4_lua=$agi_cv_with_lua
+  ])])])
+])
 
-with_auto4_lua=${agi_cv_with_lua:-no}
 AS_IF([test x$with_auto4_lua = xyes], AC_DEFINE(WITH_AUTO4_LUA, 1, [Enable Automation (auto4), requires lua]))
 
 AC_SUBST(with_auto4_lua)
 AC_SUBST(LUA_CFLAGS)
-AC_SUBST(LUA_LDFLAGS)
+AC_SUBST(LUA_LIBS)
 
 ################
 # Widget support
diff --git a/aegisub/m4macros/agi_find_libheader.m4 b/aegisub/m4macros/agi_find_libheader.m4
index 6e6334844..7d1dea637 100644
--- a/aegisub/m4macros/agi_find_libheader.m4
+++ b/aegisub/m4macros/agi_find_libheader.m4
@@ -28,7 +28,7 @@ AC_DEFUN([AGI_FIND_HEADER],[
 
 
 AC_DEFUN([AGI_FIND_LIB],[
-  aegisub_save_LDFLAGS="$LDFLAGS"
+  aegisub_save_LIBS="$LIBS"
 
   if test -n "$3"; then
     LDDIR="-L$3"
@@ -36,7 +36,7 @@ AC_DEFUN([AGI_FIND_LIB],[
 
   for lib in $2; do
     vlib=`echo $lib | $as_tr_sh`
-    LDFLAGS="$LDDIR -l$lib"
+    LIBS="$LDDIR -l$lib"
     AC_CACHE_CHECK(
       [for -l${lib}],
       [agi_cv_lib_${vlib}],
@@ -52,7 +52,7 @@ AC_DEFUN([AGI_FIND_LIB],[
   done
 
   if test -n "$found"; then
-    $1_LDFLAGS="$LDDIR -l$found"
+    $1_LIBS="$LDDIR -l$found"
   fi
-  LDFLAGS="$aegisub_save_LDFLAGS"
+  LIBS="$aegisub_save_LIBS"
 ])
diff --git a/aegisub/src/Makefile b/aegisub/src/Makefile
index e6141c670..120e23ffc 100644
--- a/aegisub/src/Makefile
+++ b/aegisub/src/Makefile
@@ -79,7 +79,7 @@ endif
 ifeq (yes, $(HAVE_AUTO4_LUA))
 SRC_OPT += auto4_lua.cpp auto4_lua_assfile.cpp auto4_lua_dialog.cpp auto4_lua_progresssink.cpp auto4_lua_scriptreader.cpp
 auto4_lua.o auto4_lua_assfile.o auto4_lua_dialog.o  auto4_lua_progresssink.o auto4_lua_scriptreader.o: CXXFLAGS += $(CFLAGS_LUA)
-LDFLAGS += $(LDFLAGS_LUA)
+LIBS += $(LIBS_LUA)
 endif
 
 ##############