diff --git a/e2e/config/test_hooks_config_root b/e2e/config/test_hooks_config_root
new file mode 100644
index 0000000000..80eba323da
--- /dev/null
+++ b/e2e/config/test_hooks_config_root
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+# Test that config_root in hooks correctly points to the project root
+# even when the config file is in a .mise/ subdirectory
+# See: https://github.com/jdx/mise/discussions/6531
+
+# Create project structure with .mise/config.toml
+mkdir -p .mise
+cat <<EOF >.mise/config.toml
+[hooks]
+enter = 'echo CONFIG_ROOT={{config_root}}'
+EOF
+
+# Initialize mise and go to home first
+eval "$(mise hook-env)"
+
+# Leave the workdir (go home)
+cd ~ || exit 1
+eval "$(mise hook-env)"
+
+# Now re-enter the workdir to trigger the enter hook
+cd ~/workdir || exit 1
+
+# The config_root should be ~/workdir, not ~/workdir/.mise
+assert_contains "mise hook-env 2>&1" "CONFIG_ROOT=$HOME/workdir"
+assert_not_contains "mise hook-env 2>&1" "CONFIG_ROOT=$HOME/workdir/.mise"
diff --git a/src/config/config_file/mise_toml.rs b/src/config/config_file/mise_toml.rs
index e6c522b752..e062752b5b 100644
--- a/src/config/config_file/mise_toml.rs
+++ b/src/config/config_file/mise_toml.rs
@@ -167,8 +167,10 @@ impl MiseToml {
             }
         };
         rf.context = BASE_CONTEXT.clone();
-        rf.context
-            .insert("config_root", path.parent().unwrap().to_str().unwrap());
+        rf.context.insert(
+            "config_root",
+            config_root::config_root(path).to_str().unwrap(),
+        );
         rf.update_context_env(env::PRISTINE_ENV.clone());
         rf.path = path.to_path_buf();
         let project_root = rf.project_root().map(|p| p.to_path_buf());