diff --git a/aikit b/aikit
index 8ca4a2b..30adea1 100755
--- a/aikit
+++ b/aikit
@@ -1038,6 +1038,22 @@ def save_config(config):
     CONFIG_FILE.chmod(0o600)
 
 
+def _validate_config_patch(patch):
+    """Validate a POST /api/config body. Returns an error string or None."""
+    if not isinstance(patch, dict):
+        return "Request body must be a JSON object"
+    unknown = set(patch) - set(DEFAULT_CONFIG)
+    if unknown:
+        return f"Unknown config keys: {', '.join(sorted(unknown))}"
+    if "version" in patch and not isinstance(patch["version"], int):
+        return "version must be an integer"
+    if "agents" in patch and not isinstance(patch["agents"], dict):
+        return "agents must be an object"
+    if "settings" in patch and not isinstance(patch["settings"], dict):
+        return "settings must be an object"
+    return None
+
+
 def _needs_setup():
     return not SETUP_MARKER.exists()
 
@@ -5061,12 +5077,13 @@ def create_flask_app():
     @app.route("/api/config", methods=["GET", "POST"])
     def api_config():
         if request.method == "POST":
-            try:
-                new_config = request.get_json()
-                save_config(new_config)
-                return jsonify({"ok": True})
-            except Exception as e:
-                return jsonify({"error": str(e)}), 400
+            patch = request.get_json(silent=True)
+            err = _validate_config_patch(patch)
+            if err:
+                return jsonify({"error": err}), 400
+            config = load_config()
+            save_config(_deep_merge(config, patch))
+            return jsonify({"ok": True})
 
         config = load_config()
         def mask(obj):
diff --git a/docs/aikit.md b/docs/aikit.md
index b06cc77..08c09e2 100644
--- a/docs/aikit.md
+++ b/docs/aikit.md
@@ -124,7 +124,7 @@ Dashboard features:
 | `/api/install/<key>` | POST | Install an agent |
 | `/api/update/<key>` | POST | Update an agent |
 | `/api/doctor` | GET | Environment diagnostics |
-| `/api/config` | GET/POST | Read/update configuration |
+| `/api/config` | GET/POST | Read config (GET) or deep-merge a partial update (POST) |
 
 ---
 
@@ -143,6 +143,12 @@ aikit config get settings.web_port   # Get a specific value
 aikit config set settings.web_port 9000  # Set a value
 ```
 
+`POST /api/config` accepts a partial JSON object and **deep-merges** it into the
+loaded config (same semantics as `aikit config set` for nested keys). Only known
+top-level keys (`version`, `agents`, `settings`) are accepted; unknown keys or
+wrong types return HTTP 400. An empty nested object (e.g. `"agents": {}`) does
+not wipe sibling keys under that section.
+
 ---
 
 ## Gateway
diff --git a/tests/test_aikit_api_config.py b/tests/test_aikit_api_config.py
new file mode 100644
index 0000000..0e85c73
--- /dev/null
+++ b/tests/test_aikit_api_config.py
@@ -0,0 +1,81 @@
+"""Tests for aikit POST /api/config deep-merge and validation."""
+
+from __future__ import annotations
+
+import json
+
+import pytest
+
+
+@pytest.fixture
+def aikit_app(tool_loader, tmp_path, monkeypatch):
+    m = tool_loader("aikit")
+    config_dir = tmp_path / ".aikit"
+    config_file = config_dir / "config.json"
+    monkeypatch.setattr(m, "CONFIG_DIR", config_dir)
+    monkeypatch.setattr(m, "CONFIG_FILE", config_file)
+    monkeypatch.delenv("AIKIT_SETTINGS__WEB_PORT", raising=False)
+    app = m.create_flask_app()
+    app.config["TESTING"] = True
+    return m, app.test_client(), config_file
+
+
+def _write_config(path, data):
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(json.dumps(data, indent=2) + "\n")
+
+
+def test_api_config_post_deep_merges_settings(aikit_app):
+    m, client, config_file = aikit_app
+    _write_config(config_file, {
+        "version": 1,
+        "agents": {"cursor": {"installed": True, "version": "1.0"}},
+        "settings": {"web_port": 8765, "web_host": "localhost"},
+    })
+
+    resp = client.post(
+        "/api/config",
+        json={"settings": {"web_port": 8801}, "version": 1, "agents": {}},
+    )
+    assert resp.status_code == 200
+    assert resp.get_json() == {"ok": True}
+
+    saved = json.loads(config_file.read_text())
+    assert saved["settings"]["web_port"] == 8801
+    assert saved["settings"]["web_host"] == "localhost"
+    assert saved["agents"] == {"cursor": {"installed": True, "version": "1.0"}}
+
+
+def test_api_config_post_rejects_unknown_keys(aikit_app):
+    _, client, config_file = aikit_app
+    _write_config(config_file, {"version": 1, "agents": {}, "settings": {}})
+
+    resp = client.post("/api/config", json={"bogus": 1})
+    assert resp.status_code == 400
+    assert "Unknown config keys" in resp.get_json()["error"]
+
+
+def test_api_config_post_rejects_non_object(aikit_app):
+    _, client, _ = aikit_app
+
+    resp = client.post(
+        "/api/config",
+        data="[]",
+        content_type="application/json",
+    )
+    assert resp.status_code == 400
+    assert resp.get_json()["error"] == "Request body must be a JSON object"
+
+
+def test_api_config_post_rejects_invalid_types(aikit_app):
+    _, client, config_file = aikit_app
+    _write_config(config_file, {"version": 1, "agents": {}, "settings": {}})
+
+    resp = client.post("/api/config", json={"settings": "nope"})
+    assert resp.status_code == 400
+    assert resp.get_json()["error"] == "settings must be an object"
+
+
+def test_validate_config_patch_accepts_partial(aikit_app):
+    m, _, _ = aikit_app
+    assert m._validate_config_patch({"settings": {"web_port": 9000}}) is None