diff --git a/pkgs/development/compilers/gcc/builder.sh b/pkgs/development/compilers/gcc/builder.sh
index 2d7a058fa01..52e044ad6b5 100644
--- a/pkgs/development/compilers/gcc/builder.sh
+++ b/pkgs/development/compilers/gcc/builder.sh
@@ -250,6 +250,17 @@ postInstall() {
         done
     fi
 
+    # Cross-compiler specific:
+    # --with-headers=$dir option triggers gcc to make a private copy
+    # of $dir headers and use it later as `-isysroot`. This prevents
+    # cc-wrapper from overriding libc headers with `-idirafter`.
+    # It should be safe to drop it and rely solely on the cc-wrapper.
+    local sysinc_dir=$out/${targetConfig+$targetConfig/}sys-include
+    if [ -d "$sysinc_dir" ]; then
+        chmod -R u+w "$out/${targetConfig+$targetConfig/}sys-include"
+        rm -rfv "$out/${targetConfig+$targetConfig/}sys-include"
+    fi
+
     # Get rid of some "fixed" header files
     rm -rfv $out/lib/gcc/*/*/include-fixed/{root,linux}