Bring a large stockpot of water to a boil. Add chopped squash and onions to the pot and cook over medium heat until squash and onions are tender, about 5 minutes. Drain liquid with a colander and set aside.
Meanwhile, add eggs to a medium bowl and lightly whisk. Add cheeses, half and half, cayenne pepper, salt, and black pepper to the bowl and stir until combined.
Spray a 9x13 casserole dish with cooking spray. Pour squash mixture and egg mixture into the baking dish. Crush crackers into a large bowl and melt the butter. Add melted butter to the cracker crumbs and stir until all the crumbs are coated with the butter. Spread the crackers evenly on top of the casserole. Bake in preheated oven for about 40 minutes or until warm and bubbly around the edges and the top of the casserole is lightly toasted.
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