Preheat oven to 325 degrees F (165 degrees C). Grease a 9x9-inch baking dish.
In a large bowl, beat the eggs, and slowly whisk in whole wheat flour, baking powder, salt, garlic, red pepper flakes, and nutmeg. Mix in the cottage cheese, Cheddar cheese, and bacon. Transfer the mixture to the prepared baking dish.
Bake in the preheated oven until the top is browned and crispy, and a toothpick inserted into the center of the souffle comes out clean, 55 minutes to 1 hour.