Preheat oven to 350 degrees. Grease a muffin tin with avocado oil to prevent sticking.
Heat a large sauté pan over medium heat. Spray with avocado oil and let it get hot, about 30 seconds. Add green pepper and cook for 3 minutes, stirring occasionally. Add mushrooms and cook for another 2 minutes. Add 1/4 cup pizza sauce and mix well. Remove from heat.
In a large bowl whisk eggs together with salt and pepper.
Place pepperoni in muffin tins, creating a cup to hold the toppings. Add 1 heaping tablespoon of pepper and mushroom mixture in each cup. Repeat until muffin tin is full. Divide whisked eggs evenly among pepperoni cups. Top with a little more pizza sauce (optional) and a pinch of dried basil and red pepper flakes.
Bake for 12 minutes or until eggs are set and no longer jiggle. Let cool for a few minutes.
*make sure to check labels and ingredients are complaint if doing the Whole30.