Bring a large stockpot of water to a boil. Add chopped squash and onions to the pot and continue to cook over medium heat until squash and onions are tender, about 5 minutes.
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 with cooking spray. Pour mixture into the baking dish. Crush crackers into a medium-sized bowl. Add melted butter to the crackers and stir until all the crackers are coated with the butter. Spread the crackers evenly on top of the casserole. Place 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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