Preheat the oven to 350°F (175°C) and grease a 12-cup muffin tin with olive oil or cooking spray.
In a large mixing bowl, whisk together eggs, cottage cheese, almond flour, garlic powder, salt, and pepper until smooth.
Stir in the cheddar cheese, mozzarella, spinach, bell pepper, green onions, and mushrooms until evenly combined.
Pour the mixture into the muffin tin, filling each cup about 3/4 full.
Bake for 20-25 minutes or until the muffins are set and slightly golden on top.
Let cool for a few minutes before removing from the tin. Serve warm or store for later.