diff --git a/pkgs/development/libraries/flatpak/default.nix b/pkgs/development/libraries/flatpak/default.nix
index ceca7e24fb6e..62a9ebcd7fb3 100644
--- a/pkgs/development/libraries/flatpak/default.nix
+++ b/pkgs/development/libraries/flatpak/default.nix
@@ -1,6 +1,8 @@
 { stdenv
 , fetchurl
-, autoreconfHook
+, autoconf
+, automake
+, libtool
 , docbook_xml_dtd_412
 , docbook_xml_dtd_42
 , docbook_xml_dtd_43
@@ -104,7 +106,9 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [
-    autoreconfHook
+    autoconf
+    automake
+    libtool
     libxml2
     docbook_xml_dtd_412
     docbook_xml_dtd_42
@@ -179,6 +183,10 @@ stdenv.mkDerivation rec {
     patchShebangs tests
   '';
 
+  preConfigure = ''
+    NOCONFIGURE=1 ./autogen.sh
+  '';
+
   passthru = {
     tests = {
       installedTests = nixosTests.installed-tests.flatpak;