Preheat your oven to 375°F (190°C) and lightly grease a 9-inch baking dish with the olive oil.
Thinly slice the zucchini and summer squash into uniform rounds using a sharp knife or a mandoline for even cooking.
In a medium mixing bowl, whisk together the egg whites, whole egg, Greek yogurt, garlic powder, onion powder, sea salt, and black pepper until the mixture is completely smooth.
Arrange the squash and zucchini slices in the prepared baking dish, overlapping them slightly in concentric circles or rows.
Pour the egg and yogurt mixture evenly over the vegetables, gently shaking the dish to ensure the liquid settles between the layers.
In a small bowl, combine the almond flour, parmesan cheese, and fresh thyme, then sprinkle this topping evenly over the gratin.
Bake for 35 to 40 minutes until the custard is set and the almond-parmesan crust has turned a beautiful golden brown.