diff --git a/pkgs/build-support/fetchgit/nix-prefetch-git b/pkgs/build-support/fetchgit/nix-prefetch-git
index f2d36f54a2d5..5e78dcc72b84 100755
--- a/pkgs/build-support/fetchgit/nix-prefetch-git
+++ b/pkgs/build-support/fetchgit/nix-prefetch-git
@@ -123,10 +123,6 @@ fi
 init_remote(){
     local url=$1
     clean_git init --initial-branch=master
-    # Disable maintenance: it's not useful for a short-lived clone, and
-    # background maintenance causes non-deterministic builds.
-    # https://github.com/NixOS/nixpkgs/issues/524215
-    clean_git config maintenance.auto false
     clean_git remote add origin "$url"
     if [ -n "$sparseCheckout" ]; then
         git config remote.origin.partialclonefilter "blob:none"
@@ -518,6 +514,15 @@ HOME="$tmpHomePath"
 unset XDG_CONFIG_HOME
 export GIT_CONFIG_NOSYSTEM=1
 
+
+# Disable maintenance: it's not useful for a short-lived clone, and
+# background maintenance causes non-deterministic builds.
+# https://github.com/NixOS/nixpkgs/issues/524215
+export GIT_CONFIG_COUNT=$(( ${GIT_CONFIG_COUNT:-0} + 1 ))
+# Not the best but generic enough that it will work with `impureEnvVars`
+export "GIT_CONFIG_KEY_$(( GIT_CONFIG_COUNT - 1 ))=maintenance.auto"
+export "GIT_CONFIG_VALUE_$(( GIT_CONFIG_COUNT - 1 ))=false"
+
 if test -n "$builder"; then
     test -n "$out" -a -n "$url" -a -n "$rev" || usage
     if test -n "$rootDir"; then