baked egg muffin cups
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Easy Baked Egg Muffin Cups

Whole wheat tortilla shells make these egg cups super easy to serve.
Prep Time20 mins
Cook Time15 mins
Course: Breakfast
Cuisine: American
Keyword: eggs, muffins, tortilla shells
Servings: 8 egg cups
Author: Trish | The In Fine Balance Food Blog



  • 8 whole wheat small tortillas
  • 4 eggs
  • 1/4 cup milk
  • salt and pepper
  • 1 red pepper, diced
  • 1 small red onion, diced
  • 1/2 cup shredded heese – cheddar or a Tex-Mex mix of some sort
  • green onions
  • fresh tomato
  • cilantro
  • Greek yogurt or sour cream
  • salsa


  • Preheat oven to 400 degrees.  Coat your muffin tray with cooking spray.
  • Using 8 small whole wheat tortillas stuff your muffin cups. I wanted to cut each tortilla in half, and so only use 4, but my husband was in charge of the cup stuffing and he is a "more is better kind of guy” – so we used a whole small tortilla for each muffin cup.  You can see from the picture how he pushed them into the tins.
  • Make a “scrambled” egg mixture – however you like your scrambled eggs.  We used 4 large eggs with a splash of milk, salt and pepper. You could also just use egg whites. Set this aside.
  • Heat a non-stick skillet or frying pan over medium heat.  Add a touch of olive oil if needed.
  • Dice one red pepper and one small red onion and sauté until soft. We seasoned ours with a Tex-Mex spice blend.
  • Meanwhile, dice and seed a tomato or two, chopped some green onions and cilantro.
  • Assemble the egg cups.
  • In each tortilla shell add a heaping tablespoon of the red pepper and onion mixture.  Top with a few pieces of tomato, a sprinkle of cilantro and some green onion. Pour egg mixture on top, until muffin tin (not the tortilla shell) is almost full.  Sprinkle shredded cheese on top of each.
  • Bake for about 15 minutes, or until the eggs are set and the tortilla is nicely browned.
  • Top with Greek yogurt or sour cream and salsa.