diff --git a/justfile b/justfile
index e92b5fb5f..ca02c4db3 100644
--- a/justfile
+++ b/justfile
@@ -74,13 +74,28 @@ prek-install-git-pre-commit-hook: _ensure_mise_tools_installed
     #!/usr/bin/env sh
     set -eu
     {{ just_executable() }} --justfile "{{ justfile() }}" mise exec -- prek install
-    hook="{{ justfile_directory() }}/.git/hooks/pre-commit"
-    # The installed git hook runs later under Git, outside this just/mise environment.
-    # Injecting PREK_HOME keeps prek's cache under var/prek instead of a global home dir,
-    # which is more predictable and works better in sandboxed tools like Codex/OpenCode.
-    if [ -f "$hook" ] && ! grep -q '^export PREK_HOME=' "$hook"; then
-        sed -i '2iexport PREK_HOME="{{ prek_home }}"' "$hook"
-    fi
+    # The installed git hooks run later under Git, outside this just/mise environment,
+    # so they need to be told how to find their tooling:
+    #
+    # - PREK_HOME keeps prek's cache under var/prek instead of a global home dir.
+    # - MISE_DATA_DIR / MISE_TRUSTED_CONFIG_PATHS make mise resolve against this project's
+    #   own data directory. Without them mise falls back to the global one and silently
+    #   installs a second copy of the tool there.
+    # - prek bakes the full path of the currently installed version into the hook
+    #   (var/mise/installs/prek/<version>/...), which stops working as soon as the pinned
+    #   version changes or old versions are pruned. Pointing at mise's shim instead makes
+    #   the hook resolve whatever mise.toml pins, at the time it runs.
+    #
+    # Which hook files prek installs depends on `default_install_hook_types` in
+    # .pre-commit-config.yaml, so patch every hook file that prek generated.
+    for hook in "{{ justfile_directory() }}"/.git/hooks/*; do
+        [ -f "$hook" ] || continue
+        grep -q 'generated by prek' "$hook" || continue
+        grep -q '^export PREK_HOME=' "$hook" || sed -i '2iexport PREK_HOME="{{ prek_home }}"' "$hook"
+        grep -q '^export MISE_DATA_DIR=' "$hook" || sed -i '3iexport MISE_DATA_DIR="{{ mise_data_dir }}"' "$hook"
+        grep -q '^export MISE_TRUSTED_CONFIG_PATHS=' "$hook" || sed -i '4iexport MISE_TRUSTED_CONFIG_PATHS="{{ mise_trusted_config_paths }}"' "$hook"
+        sed -i 's#^PREK=".*"$#PREK="{{ mise_data_dir }}/shims/prek"#' "$hook"
+    done
 
 # Runs the playbook with --tags=install-all,ensure-matrix-users-created,start and optional arguments
 install-all *extra_args: (run-tags "install-all,ensure-matrix-users-created,start" extra_args)