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Get It NowMake 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.
Why You’ll Love My Egg Muffin Cups
- Taste like an omelette – These have all the fluffy texture of my omelette recipe, but in portable form… for those days you want eggs, but need the grab-and-go factor.
- Super easy to make – Just cook your favorite 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. Helpful if you’re always doing a bunch of things at once like I am!
- Totally customizable – Make your egg muffin cups with vegetables, meats, cheeses, or any combination of these! I picked veggies for 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… or you know, reach for them when you realize you had no plan. I always try to keep some in my freezer.
- Healthy breakfast – Egg muffins are packed with protein and vegetables (a.k.a. my requirements for a meal), so they are 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 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
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’re 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. 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.)
- 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!
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:
- 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 – Make my sauteed mushrooms and add 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. Fresh spinach is very watery, so for spinach egg muffin cups, I use either sauteed spinach or frozen spinach drained well.
- 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.
- 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 (my fave), or Mexican blend cheese.
- 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.
- 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.
- 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.
- 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.
- 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.)
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.
More Healthy Egg Recipes
If you like these egg muffin cups, you might also like some of my other easy egg recipes:
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.
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.
Ingredients
Tap underlined ingredients to see where to get them.
Instructions
Tap on the times in the instructions below to start a kitchen timer while you cook.
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Preheat the oven to 400 degrees F (204 degrees C). Line a baking sheet with parchment paper or foil (grease if using foil).
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In a large bowl, toss together the broccoli, cauliflower, red pepper, minced garlic, and olive oil.
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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.
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Meanwhile, line a muffin tin with 12 parchment muffin liners or silicone muffin liners.
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When the vegetables are done, keep the oven on. Arrange the veggies evenly in the muffin cups.
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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.
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Bake for 15-20 minutes, until the eggs are set.
Did You Like It?
Leave a rating to help other readers, or get the recipe sent to your inbox.
Recipe Notes
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.
© Copyright Maya Krampf for Wholesome Yum. Please DO NOT SCREENSHOT OR COPY/PASTE recipes to social media or websites. We’d LOVE for you to share a link with photo instead. 🙂
103 Comments
Claire
0These came out incredible! I’ve made multiple variations now, and they’re all so good! My first time they were delicious, but i made the mistake of using cupcake papers. They stick. I don’t suggest it. The second time I forgot the cheese, but i used silicone cupcake pans and they came out beautifully. This last time, i roasted cauliflower, broccoli, garlic, scallions, and zucchini in a glass 11×13 pan for 25 minutes. (I had a bunch of extra veggies, so i cooked them longer) After they baked, I added the Cheddar (i refused to forget it this time) and added the egg mixture right on top and baked it for 20 minutes at 400. So freaking good! I’ve been using a garlic/pepper/seasalt grill seasoning and they’re extra flavorful. Thank you for making my mornings healthier and way more manageable!
Krissy
0Made these for the kids this week since they’re always running out the door without breakfast. They loved them and kept them fueled til lunchtime!
Sha
0These are adorable and delicious! Glad they’re healthy!
Jana R
0I have been making these for so long. My whole family loves them and they are totally customizable too!
Ann Wittman
0I made this today for lunch… delicious!!! I plan on trying it again next weekend with my grandkids. I’m sure they’ll love it!
Aspen Jacquet
0I made these for breakfast this morning for my mom and I and they were delightful! I put bacon, caramelized onions, scallions, bell peppers, and basil. They were so delicious and easy to make. They would be really good for breakfast meal prep too. I even left out the milk and just added an extra egg and they turned out perfectly fluffy. 10/10 definitely give these a try!
Wait Pamela
0I am trying to follow a low carb diet so I made these Egg Muffin cups. What a game changer! Besides being delicious, they keep well in the fridge and they freeze well. My sisters and I travel quite a bit and I will take these frozen muffins and eat them along the way. (They are even good slightly frozen.) We like ham and cheese and asparagus the best, but we have even used leftover ground beef and cheese for a cheeseburger taste. There are so many different foods we can add, I don’t think we will ever get tired of them. YUM
Olga Fedorchuk
0These are great to have on hand for a quick snack as well as a meal. Very tasty and I mix up the vegetables and cheese, depending on what I have on hand.
Mary
0These muffins is going to be an amazing addition to my breakfast menu. These muffins have a wonderful bite. Will definitely be making again. At 2.5 grams of carbs I can use as a snack. Being diabetic for me its hard to find things I can have or will eat.
Julieta Maile
0I haven’t tried yet but I think this is lovely,. I will definitely make it for breakfast. Thank you.
Charles W
0These egg muffins cups taste great and are perfect for a quick keto meal. I batch cook a dozen and freeze. I use whatever veggies I have and cycle through bacon mushroom, sausage mushroom, and mexican using taco meat(dollop of sour cream and salsa on top!). Great for breakfast, brunch or lunch. Heat and serve on a bed of fresh spinach drizzled with olive oil.
Tonya Jasper
0It is an absolutely delicious recipe! I used extra broccoli since I didn’t have cauliflower. I also forgot to add the heavy cream, but they still tasted amazing, and I will try following the recipe perfectly next time. Thanks for sharing!
Lucinda
0Made these using my fresh eggs, from backyard chickens. Added mini sweet peppers, fresh ground homemade sausage, Colby Jack cheese, mushrooms, and fresh spinach. My husband’s 4man workcrew devoured 24 in one sitting and asked me to make more. They were a total success, thank you.
Margi
0Trying tomorrow morning. Looks good. Thanks and I’ll let you know.
Erin Stuedemann
0Made these the other day for something quick, nutritious and hearty to warm up and eat before work in the mornings. They were delicious! I will definitely be trying the other variations because they were so easy and tasted great!
Bobbi Toner
0I eat lots of eggs. Sounds delicious.
Gail Ouellette
0I made these two ways, one in the muffin tins and I had so much filling leftover (did a double batch) and did the rest in a 9×9 pan. I love the muffin ones…so easy for grab and go. I made mine with mushroom, sausage, bacon and cheddar cheese…so yummy! Thanks for another great and versatile recipe.
Julia
0I made two different versions and both were delicious. First was protein heavy with breakfast sausage and bacon and pepper jack cheese the second was mushroom, onion and peppers with Mexican cheese. Easy to make and to reheat for a quick meal.
Ronn
0Haven’t made this yet, but I’ve saved the recipe because it sounds Yummy!! Thanks!
Katia
0These were the best egg muffins we’ve ever had!
Question: I signed up for plus for the automated meal planning and shopping list… Is there a way to make the meal plan give automated vegetarian options instead each week? I know I can switch them out to my own recipes I choose from the app. Just wondering if there is a button for that somewhere that I’m missing. It would really simplify things for me even more if there was a way to do that.
Wholesome Yum D
0Hi Katia, We currently only offer 1 meal plan per week, maybe in the future we could offer meal plans for different diets.
Anita
0Perfect recipe to use for my daughter’s and I. I can keep it gluten and lactose free. This is now our go to breakfast! Thank you for posting it! 😋😋😋