Preheat your oven to 350°F (175°C).

Heat olive oil in a medium skillet over medium heat. Add the sliced onions and minced garlic, stirring frequently for about 5 to 7 minutes until soft and translucent.

While the onions and garlic are sautéing, thinly slice the zucchini and yellow squash to about ¼ inch thick. Set aside.

In a greased baking dish, start layering the sliced zucchini and yellow squash with the sautéed onion and garlic mixture.

In a bowl, whisk together the heavy cream, Gruyère cheese, Parmesan cheese, fresh thyme, salt, and pepper until well blended.

Pour the cream mixture evenly over the layered vegetables in the baking dish.

Bake in the preheated oven for about 40 minutes until the top is golden brown and bubbly.

Allow the gratin to rest for about 10 minutes before serving.