diff --git a/pkgs/by-name/li/libiberty/package.nix b/pkgs/by-name/li/libiberty/package.nix
index 2040ef3bee08..fc7584e484df 100644
--- a/pkgs/by-name/li/libiberty/package.nix
+++ b/pkgs/by-name/li/libiberty/package.nix
@@ -14,6 +14,12 @@ stdenv.mkDerivation {
 
   postUnpack = "sourceRoot=\${sourceRoot}/libiberty";
 
+  # needed until config scripts are updated to not use /usr/bin/uname on FreeBSD native
+  # updateAutotoolsGnuConfigScriptsHook doesn't seem to work here
+  postPatch = ''
+    substituteInPlace ../config.guess --replace-fail /usr/bin/uname uname
+  '';
+
   configureFlags = [ "--enable-install-libiberty" ]
     ++ lib.optional (!staticBuild) "--enable-shared";
 
diff --git a/pkgs/by-name/li/libmpc/package.nix b/pkgs/by-name/li/libmpc/package.nix
index 053f0113b444..eaa5943ffe14 100644
--- a/pkgs/by-name/li/libmpc/package.nix
+++ b/pkgs/by-name/li/libmpc/package.nix
@@ -1,5 +1,6 @@
 { lib, stdenv, fetchurl
 , gmp, mpfr
+, updateAutotoolsGnuConfigScriptsHook
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -20,6 +21,10 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   buildInputs = [ gmp mpfr ];
+  nativeBuildInputs = [
+    # needed until config scripts are updated to not use /usr/bin/uname on FreeBSD native
+    updateAutotoolsGnuConfigScriptsHook
+  ];
 
   doCheck = true; # not cross;
 
diff --git a/pkgs/development/compilers/llvm/common/llvm/default.nix b/pkgs/development/compilers/llvm/common/llvm/default.nix
index 637c47770c5f..1b90522a4ebf 100644
--- a/pkgs/development/compilers/llvm/common/llvm/default.nix
+++ b/pkgs/development/compilers/llvm/common/llvm/default.nix
@@ -24,6 +24,7 @@
 , which
 , sysctl
 , buildLlvmTools
+, updateAutotoolsGnuConfigScriptsHook
 , debugVersion ? false
 , doCheck ? !stdenv.hostPlatform.isAarch32 && (if lib.versionOlder release_version "15" then stdenv.hostPlatform.isLinux else true)
   && (!stdenv.hostPlatform.isx86_32 /* TODO: why */) && (!stdenv.hostPlatform.isMusl)
@@ -112,7 +113,12 @@ stdenv.mkDerivation (finalAttrs: {
     "shadowstack"
   ];
 
-  nativeBuildInputs = [ cmake ]
+  nativeBuildInputs = [
+    cmake
+    # while this is not an autotools build, it still includes a config.guess
+    # this is needed until scripts are updated to not use /usr/bin/uname on FreeBSD native
+    updateAutotoolsGnuConfigScriptsHook
+  ]
     ++ (lib.optional (lib.versionAtLeast release_version "15") ninja)
     ++ [ python ]
     ++ optionals enableManpages [
diff --git a/pkgs/development/libraries/isl/generic.nix b/pkgs/development/libraries/isl/generic.nix
index 8974839dca26..e8612a916532 100644
--- a/pkgs/development/libraries/isl/generic.nix
+++ b/pkgs/development/libraries/isl/generic.nix
@@ -11,6 +11,7 @@
 , gmp
 , autoreconfHook
 , buildPackages
+, updateAutotoolsGnuConfigScriptsHook
 }:
 
 stdenv.mkDerivation {
@@ -25,7 +26,12 @@ stdenv.mkDerivation {
 
   strictDeps = true;
   depsBuildBuild = lib.optionals (lib.versionAtLeast version "0.24") [ buildPackages.stdenv.cc ];
-  nativeBuildInputs = lib.optionals (stdenv.hostPlatform.isRiscV && lib.versionOlder version "0.24") [ autoreconfHook ];
+  nativeBuildInputs = lib.optionals (stdenv.hostPlatform.isRiscV && lib.versionOlder version "0.24") [
+    autoreconfHook
+  ] ++ [
+    # needed until config scripts are updated to not use /usr/bin/uname on FreeBSD native
+    updateAutotoolsGnuConfigScriptsHook
+  ];
   buildInputs = [ gmp ];
 
   inherit configureFlags;