diff --git a/pkgs/development/tools/misc/babeltrace/default.nix b/pkgs/development/tools/misc/babeltrace/default.nix
index 3dc424f106bf..014d926eea3d 100644
--- a/pkgs/development/tools/misc/babeltrace/default.nix
+++ b/pkgs/development/tools/misc/babeltrace/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, pkg-config, glib, libuuid, popt, elfutils }:
+{ lib, stdenv, fetchurl, autoreconfHook, pkg-config, glib, libuuid, popt, elfutils }:
 
 stdenv.mkDerivation rec {
   pname = "babeltrace";
@@ -9,9 +9,18 @@ stdenv.mkDerivation rec {
     sha256 = "1hkg3phnamxfrhwzmiiirbhdgckzfkqwhajl0lmr1wfps7j47wcz";
   };
 
-  nativeBuildInputs = [ pkg-config ];
+  # The pre-generated ./configure script uses an old autoconf version which
+  # breaks cross-compilation (replaces references to malloc with rpl_malloc).
+  # Re-generate with nixpkgs's autoconf. This requires glib to be present in
+  # nativeBuildInputs for its m4 macros to be present.
+  nativeBuildInputs = [ autoreconfHook glib pkg-config ];
   buildInputs = [ glib libuuid popt elfutils ];
 
+  # --enable-debug-info (default) requires the configure script to run host
+  # executables to determine the elfutils library version, which cannot be done
+  # while cross compiling.
+  configureFlags = lib.optional (stdenv.hostPlatform != stdenv.buildPlatform) "--disable-debug-info";
+
   meta = with lib; {
     description = "Command-line tool and library to read and convert LTTng tracefiles";
     homepage = "https://www.efficios.com/babeltrace";