diff --git a/crates/picloud-cli/tests/apply.rs b/crates/picloud-cli/tests/apply.rs
index 771b355..52b1d77 100644
--- a/crates/picloud-cli/tests/apply.rs
+++ b/crates/picloud-cli/tests/apply.rs
@@ -151,3 +151,105 @@ fn apply_rejects_bad_bundle_atomically() {
         "a failed apply must leave nothing behind:\n{s}"
     );
 }
+
+#[ignore = "needs DATABASE_URL pointing at a running Postgres"]
+#[test]
+fn apply_reconciles_app_vars() {
+    let Some(fx) = common::fixture_or_skip() else {
+        return;
+    };
+    let env = common::admin_env(fx);
+    let slug = common::unique_slug("apply-vars");
+    common::pic_as(&env)
+        .args(["apps", "create", &slug])
+        .assert()
+        .success();
+    let _guard = AppGuard::new(&env.url, &env.token, &slug);
+
+    let dir = manifest_dir();
+    // The script returns the resolved `region` var verbatim, so an invoke
+    // reflects exactly what `apply` wrote.
+    fs::write(
+        dir.path().join("scripts/read.rhai"),
+        "vars::get(\"region\")",
+    )
+    .unwrap();
+    let manifest = |vars_block: &str| {
+        format!(
+            "[app]\nslug = \"{slug}\"\nname = \"Vars Test\"\n\n\
+             [[scripts]]\nname = \"read\"\nfile = \"scripts/read.rhai\"\n\n\
+             [[routes]]\nscript = \"read\"\nmethod = \"POST\"\n\
+             host_kind = \"any\"\npath_kind = \"exact\"\npath = \"/read\"\n\n\
+             {vars_block}"
+        )
+    };
+    let manifest_path = dir.path().join("picloud.toml");
+
+    // 1. Apply with `region = "eu"` → the var is created and injected.
+    fs::write(&manifest_path, manifest("[vars]\nregion = \"eu\"\n")).unwrap();
+    let out = common::pic_as(&env)
+        .args(["apply", "--file"])
+        .arg(&manifest_path)
+        .output()
+        .expect("apply");
+    assert!(
+        out.status.success(),
+        "apply failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+    let id = script_id(&env, &slug);
+    assert_eq!(
+        invoke_body(&env, &id),
+        serde_json::json!("eu"),
+        "var applied"
+    );
+
+    // 2. Change the value → Update (not Create).
+    fs::write(&manifest_path, manifest("[vars]\nregion = \"us\"\n")).unwrap();
+    common::pic_as(&env)
+        .args(["apply", "--file"])
+        .arg(&manifest_path)
+        .assert()
+        .success();
+    assert_eq!(
+        invoke_body(&env, &id),
+        serde_json::json!("us"),
+        "var updated"
+    );
+
+    // 3. Drop the var + `--prune` → Delete; `vars::get` now returns `()`.
+    fs::write(&manifest_path, manifest("")).unwrap();
+    common::pic_as(&env)
+        .args(["apply", "--file"])
+        .arg(&manifest_path)
+        .args(["--prune", "--yes"])
+        .assert()
+        .success();
+    assert_eq!(
+        invoke_body(&env, &id),
+        serde_json::Value::Null,
+        "var pruned → unresolved"
+    );
+}
+
+fn script_id(env: &common::TestEnv, slug: &str) -> String {
+    let ls = common::pic_as(env)
+        .args(["scripts", "ls", "--app", slug])
+        .output()
+        .expect("scripts ls");
+    common::parse_first_id(std::str::from_utf8(&ls.stdout).unwrap())
+        .expect("scripts ls should produce one row")
+}
+
+fn invoke_body(env: &common::TestEnv, id: &str) -> serde_json::Value {
+    let out = common::pic_as(env)
+        .args(["scripts", "invoke", id])
+        .output()
+        .expect("scripts invoke");
+    assert!(
+        out.status.success(),
+        "invoke failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+    serde_json::from_slice(&out.stdout).expect("invoke body is JSON")
+}