Preheat oven to 325 degrees and grease 18 muffin cups.
Prep onions and pepperoni.
Break eggs into a large bowl and whisk well.
Add oregano, basil, sea salt, and freshly ground black pepper. Mix well.
Heat coconut oil in a skillet over medium heat. Once hot, sautee onion and minced garlic.
Once soft, add tomato paste, diced tomatoes, pepperoni, and chipotle chili powder. Cook 2-4 minutes longer until all ingredients are heated through.
Fill greased muffin cups about a quarter of the way with the onion/tomato/pepperoni mixture. Cover with one layer of sliced mushroom, then pour the egg mixture in to about three quarters full.
Bake for about 30 minutes or until toothpick comes out clean.