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One batch of these 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 get to your home office computer like me. Pair them with some 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.
Why You’ll Love These Egg Muffin Cups
- Taste delicious – With a fluffy texture (kind of like an omelette in a cup) and your favorite fillings, you can’t go wrong.
- Super easy to make – Just cook your fillings, whisk the egg base, combine, and bake. Even my kids like to help me prepare them.
- Quick prep time – Most of the time to make these is hands-off, so you can do other things while they cook.
- Totally customizable – Make egg muffin cups with vegetables, meats, cheeses, or any combination of these! I picked veggies when I took these pictures, but have made them every which way over the years.
- Perfect for meal prep – They store and even freeze well, so you can plan ahead for hectic mornings.
- Healthy breakfast – These are packed with protein and vegetables, and naturally low carb and gluten free.
Ingredients & Substitutions
This section explains how to choose the best ingredients for egg muffin cups, what each one does in the recipe, and substitution options. For measurements, see the recipe card below.
- 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 crumbled oven bacon instead of some of the veggies.
- Aromatics – Not required, but I love adding some minced garlic. 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
This section shows step-by-step photos together with the instructions, to help you visualize the recipe. For full instructions, including amounts and temperatures, see the recipe card below.
- 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 are making your egg muffin cups with bacon, sausage, or other meats, pre-cook these as well.
- 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.
- Whisk the egg base. 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 egg muffin cups. (Alternatively, you can sprinkle the cheese over the other fillings and then pour the rest of the egg mixture on top.)
- Bake. They are ready when the eggs are set.
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. 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.
15 Filling Variations
One of the best things about this egg muffin cups recipe is that it’s so versatile and easy to customize to your taste. Try these combinations for add-ins:
- Ham & Cheese – Diced ham and chopped American (or cheddar) cheese.
- Peas & Carrots – My kids’ favorite combination! This one is convenient because you can just quickly saute a bag of frozen peas and carrots.
- Bacon Cheddar – Classic cooked bacon and shredded cheddar (but really, almost any cheese goes with bacon!).
- Mushroom Swiss – Sauteed mushrooms and shredded Swiss cheese.
- Asparagus Gruyere – Chopped cooked asparagus (a great way to use up leftover roasted asparagus!) and shredded Gruyere cheese.
- Spinach Feta – Spinach and crumbled feta cheese. Spinach is very watery, so for spinach egg muffin cups, use either fresh sauteed spinach or frozen spinach drained well.
- Garden Veggie – Bell peppers, mushrooms, onions, and chopped tomatoes (pat very dry and omit seedy parts). Cook the mushrooms and peppers, but not the tomatoes.
- Greek Inspired – Cooked bell peppers and red onions, sliced olives, fresh basil, and crumbled feta cheese.
- Pizza – Chopped pepperoni and shredded mozzarella. Dip in marinara sauce for serving.
- Tex-Mex – Cooked chorizo, sauteed or roasted bell peppers, and choose from Pepper Jack, Cotija, or Mexican blend cheese.
- Jalapeno Popper – Cooked bacon, chopped jalapeno peppers, sliced green onions, shredded cheddar, and small pieces of cream cheese. You only have to pre-cook the bacon (try oven bacon or air fryer bacon as hands-off methods) for this one.
- Meat Lover’s – Sausage, pepperoni, Canadian bacon, and either cheddar or mozzarella (or both!). You can also just make simpler sausage egg muffins without the other meats.
- Sun-Dried Tomato & Zucchini – Sauteed zucchini, sun-dried tomatoes, and goat cheese. You’ll need to cook down the zucchini a lot, otherwise it has a tendency to get watery.
- Garlic Parmesan – Sauteed minced garlic, Italian seasoning (or fresh herbs like pasley and chives), and shredded parmesan cheese. This version is missing bulky add-ins, so add 3-4 more eggs and an extra tablespoon or two of milk/cream to make up for it.
- Salmon – Smoked salmon or lox, capers, fresh dill, fresh chives, and dollops of cream cheese.
THE PERFECT RATIO: For 12 egg muffin cups, use 8 eggs, 1/4 cup milk of choice, 3/4 cup cheese, and 2-2.5 cups of add-ins.
The volume for the add-ins is after cooking, so you’ll start with more. (About 3 cups of most vegetables will make 2-2.5 cups cooked.)
Storage & Reheating
- Store: Keep extras in an airtight container in the refrigerator for up to 5 days.
- Meal prep: These are awesome for meal prep, so you can definitely make a batch ahead for quick breakfasts or snacks! Alternatively, you can cook the add-ins (vegetables and/or meats) ahead of time and bake them fresh.
- Reheat: For the fastest option (that I usually go for), warm them up in the microwave for about 30 seconds each. You can also heat them in the oven at 350 degrees F, which will give you a better texture but takes more time (about 10 minutes). Be careful not to overcook, or they will be rubbery.
- Freeze: Let the baked egg muffin cups cool completely first. Wrap them individually in plastic wrap, transfer to a zip lock bag, and keep in the freezer for up to 3 months. While I’ve reheated them from frozen in a pinch, they taste much better if you let them thaw in the fridge overnight before reheating.
More Healthy Egg Recipes
If you like these egg muffin cups, you might also like some of these other egg recipes:
Tools You’ll Need
- 3-Compartment Meal Prep Containers – Pop a few egg muffin cups in here with a side of green salad and some nuts, and you’ve got a nutritious breakfast that’s quicker than the drive-thru. I love that they are glass.
- Muffin Tin – This recipe is written for a regular-sized muffin tin (this one is my favorite), but you can easily use a mini muffin tin. You’ll get about twice as many muffins and the cook time will be much faster.
- Muffin Liners – A must for easy cleanup! You can use silicone muffin liners or parchment paper liners.
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.
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Tap underlined ingredients to see where to get them.
Tap on the times in the instructions below to start a kitchen timer while you cook.
In a large bowl, toss together the broccoli, cauliflower, red pepper, minced garlic, and olive oil.
Arrange the vegetables in a single layer on the baking sheet. Roast in the preheated oven for 15-20 minutes, until the edges of the broccoli are browned.
When the vegetables are done, keep the oven on. Arrange the veggies evenly in the muffin cups.
Whisk together the eggs, heavy cream, sea salt, and black pepper. Stir in the cheddar cheese. Pour the egg mixture into the muffin cups over the vegetables.
Bake for 15-20 minutes, until the eggs are set.
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Serving size: 1 egg muffin
For other flavor options and the formula to use any fillings you want, see the blog post above.
Nutrition facts are provided as a courtesy. Have questions about calculations or why you got a different result? Please see our nutrition policy.
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