Egg Muffin Cups

Ingredients & Substitutions

Here I explain the best ingredients for egg muffin cups, what each one does in the recipe, and substitution options. For measurements, see the recipe card.

• 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

I have step-by-step photos here to help you visualize the recipe. For full instructions, including amounts and temperatures, see the recipe card.

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.

15 Filling Variations

One of my favorite things about this egg muffin cups recipe is that it’s so versatile and easy to customize. I’m always making something different with them! Try these combinations for add-ins:

1. Ham & Cheese – Diced ham and chopped American (or cheddar) cheese.
2. Peas & Carrots – My kids’ favorite combination! This one is convenient because you can just quickly saute a bag of frozen peas and carrots.
3. Bacon Cheddar – Classic cooked bacon and shredded cheddar (but really, almost any cheese goes with bacon!).
4. Mushroom Swiss – Make my sauteed mushrooms and add shredded Swiss cheese.
5. Asparagus Gruyere – Chopped cooked asparagus (a great way to use up leftover roasted asparagus!) and shredded Gruyere cheese.
6. Spinach Feta – Spinach and crumbled feta cheese. Fresh spinach is very watery, so for spinach egg muffin cups, I use either sauteed spinach or frozen spinach drained well.
7. Garden Veggie – Bell peppers, mushrooms, onions, and chopped tomatoes (pat very dry and omit seedy parts). I cook the mushrooms and peppers, but not the tomatoes.
8. Greek Inspired – Cooked bell peppers and red onions, sliced olives, fresh basil, and crumbled feta cheese.
9. Pizza – Chopped pepperoni and shredded mozzarella. Dip in marinara sauce for serving.
10. Tex-Mex – Cooked chorizo, sauteed or roasted bell peppers, and choose from Pepper Jack, Cotija (my fave), or Mexican blend cheese.
11. Jalapeno Popper – I use all the components of my jalapeno poppers and tuck them inside the egg muffins: 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 my oven bacon or air fryer bacon as hands-off methods) for this one.
12. Meat Lover’s – My husband loves this one! Sausage, pepperoni, Canadian bacon, and either cheddar or mozzarella (or both!). You can also just make my simpler sausage egg muffins without the other meats.
13. Sun-Dried Tomato & Zucchini – I made a version with sauteed zucchini, sun-dried tomatoes, and goat cheese when I had leftovers from those recipes, and it was amazing! You’ll need to cook down the zucchini a lot, otherwise it tends to get watery.
14. 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 I add 3-4 more eggs and an extra tablespoon or two of milk/cream to make up for it.
15. Salmon – Smoked salmon (or my homemade lox is a treat when I have it), 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.)

Bonus: If you want a less eggy, more muffin-like texture that’s still high in protein and savory, try my cottage cheese muffins.

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! Or sometimes I just 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.

My Tools For This Recipe

• 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 – I wrote my recipe 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 – I always use these parchment paper liners for easy cleanup! You can also use silicone muffin liners.

More Healthy Egg Recipes

If you like these egg muffin cups, you might also like some of my other easy egg recipes:

Easy Peel Boiled Eggs

Egg Bites Recipe

Bacon Deviled Eggs

Egg Salad

Homemade Shakshuka

Breakfast Casserole