Egg Muffin Cups

This breakfast egg muffin cups recipe with veggies or meats, eggs, and cheese has 15 flavor options! Healthy, low carb and easy to meal prep.

Make one batch of my egg muffin cups and you’ll never want to live without them in your fridge again! Sometimes called breakfast egg muffins or mini frittatas, they make the most amazing meal prep healthy breakfast for busy days — whether you’re rushing out the door or rushing to your home office like me. Pair them with my bulletproof coffee for a filling, protein-packed morning meal. I even have a formula of ratios for you, so you can customize them to your heart’s content.

If you prefer the egg yolks and whites separate from each other, try my baked eggs in a muffin tin (very similar to these egg muffin cups, but not scrambled), or cloud eggs instead.

Ingredients & Substitutions

• Eggs – I prefer to use whole eggs, but egg whites alone work fine. To do this, replace each large egg with 3-4 tablespoons of egg whites (about 1.5 egg whites).
• Milk Or Cream – Helps the eggs get fluffy! I love the richness of heavy cream, but you can swap it for any milk of your choice, such as regular milk, half and half, coconut milk, or almond milk.
• Cheese – I use shredded cheddar most often. You can also try mozzarella, Gruyere, feta, or any other cheese you like. For a dairy-free option, simply omit the cheese (and use almond or coconut milk above).
• Fillings – I used broccoli, cauliflower, and bell peppers in the pictures and the egg muffin cups recipe card below, because that’s what I had on hand. Make it your own by choosing your favorite veggies (fresh or frozen both work fine!) and/or meats. I often make these with cooked crumbled sausage, diced ham, or chopped oven bacon instead of some of the veggies.
• Aromatics – Not required, but I love adding some minced garlic… because, um, I add it to everything. Caramelized onions would also be a delicious addition. For convenience, you could just whisk in 1/2 to 1 teaspoon of garlic powder or onion powder directly into the egg mixture.
• Olive Oil – For cooking the vegetables. Avocado oil works great, too.
• Sea Salt & Black Pepper

How To Make Egg Muffin Cups

1. Cook the add-ins. Toss the broccoli, cauliflower, red pepper, and garlic (or any other vegetables you are using) with the olive oil. Spread out in a single layer on a baking sheet and roast until edges are browned. If you’re making your egg muffin cups with bacon, sausage, or other meats, pre-cook these as well.
2. Prep the pan. Line a muffin pan with parchment paper liners or silicone cups. (You can also just spray with cooking spray, but liners make the muffins easier to remove and more portable, and require less cleanup.) Divide the roasted vegetables among the cups.
3. Whisk the egg base. In a large bowl, whisk together the eggs, heavy cream (or milk of choice), sea salt, and black pepper. Stir in cheese of your choice. Pour the mixture into the muffin wells. (Alternatively, you can sprinkle the cheese over the other fillings and then pour the rest of the egg mixture on top.)
4. Bake. Your egg muffin cups are ready when the eggs are set! Just be careful not to overcook them.

Recipe Tips & Notes

• Always pre-cook your fillings. Whether you are adding vegetables, meats, or both, you have to cook them first. If you don’t, raw meats won’t cook through properly and raw veggies will turn your egg muffin cups into a soggy, watery mess.
• You can pre-cook any way you want. I prefer roasting the vegetables because it imparts so much flavor, but any cooking method (steaming, boiling, or sauteing in a skillet) will also work. Be sure to pat dry if steaming or boiling.
• Use up leftovers. Like my chicken bacon ranch casserole, this recipe is a great way to clean out your fridge! If you have any leftover veggies or meats that are cooked from another dish, feel free to throw them in.
• Deflating a bit is normal. The air bubbles in the egg expand while baking, and they deflate as they cool. One way to reduce this effect is to let the muffins cool more slowly, so keep them in the pan to cool before removing them. I still love them even when they do shrink!