Preheat oven to 350 degrees F (175 degrees C). Grease a 9×13-inch baking dish.
Heat a large skillet over medium-high heat; cook and stir bacon and onion until bacon is evenly browned, about 10 minutes. Drain. Transfer bacon and onion to a large bowl. Stir in potatoes, eggs, Cheddar cheese, cottage cheese, and Swiss cheese. Pour mixture into prepared baking dish.
Bake in preheated oven until eggs are set and cheese is melted, 45 to 50 minutes. Let stand 10 minutes before cutting and serving.