These breakfast Egg Muffins are delicious for morning meal prep!
Protein-packed and deliciously simple, egg muffins are little handheld egg bites filled with our favorite add-ins and cheese.
We make them in batches ahead of time and reheat them throughout the week.

Make Ahead Egg Muffins
- They’re healthy, naturally gluten-free, and low in carbs.
- Egg muffins are a great way to use up any kind of leftovers, including veggies or meats.
- They’re great for meal prep! Make them ahead of time and reheat them in the microwave throughout the week.
- Egg muffin cups are perfect on their own or tucked between a couple of pieces of toast for a quick breakfast sandwich.
Ingredients in Egg Muffins
They’re so versatile; you can add almost anything to them and try new flavors every time!
Eggs – Use large whole eggs. You can also use half egg whites (from a carton) or egg substitute. I season with salt & black pepper, feel free to add other seasonings, herbs, or parsley.
Vegetables – Bell peppers and diced onion add flavor. These muffins are versatile – try mushrooms, broccoli, chopped spinach, or diced tomatoes.
Meat – Ham, sausage, or bacon are great options in these egg muffins. You can use deli ham, leftover ham, or other leftover meat.
Cheese – Sharp cheddar is a great choice for these muffins but you can use almost any kind of cheese. Pepper Jack or Monterey Jack would taste great, too!
How To Make Egg Muffins
These little egg cups are very simple to make and taste almost like mini frittatas.
- Grease the muffin tin well or use silicone liners.
- Add the add-ins to the muffin wells and top with beaten egg.
- Bake until set and enjoy!
Holly’s Quick Tips
- If adding watery veggies like mushrooms, quickly pre-cook them to remove excess moisture.
- Grease your muffin tin well or use silicone or parchment liners, the eggs tend to stick to paper liners.
- Fill the muffin cups about ¾ full. They will puff up and then fall as they cool.
- Run a butter knife along the edges to remove the eggs from the wells.
Storing, Freezing, & Reheating Egg Muffins
Refrigerator: Once baked, egg muffins can be kept in the fridge for up to 5 days.
Freezer: Egg bites can frozen for up to 3 months. Store them in an airtight container or freezer bag.
To Reheat: Microwave thawed egg muffins for 40 to 60 seconds, if heating more than one, you’ll need to increase the time. If reheating from frozen, they’ll need a bit longer, about 60-90 seconds.
More Make-Ahead Breakfast Recipes
Did your family love these Make-Ahead Egg Muffins? Be sure to leave a rating and a comment below!
Make Ahead Egg Muffins
Ingredients
- 10 large eggs *see note
- ½ teaspoon black pepper
- ¼ teaspoon salt
- ¼ teaspoon garlic powder optional
- 1 ½ cups diced ham or 8 slices bacon, cooked & crumbled or ½ lb sausage, browned
- ½ red bell pepper diced
- 3 tablespoons white onion minced, or 2 green onions, thinly sliced
- 1 cup shredded cheddar cheese or your favorite blend of shredded cheese
- ½ cup shredded mozzarella cheese
Instructions
- Preheat the oven to 350°F.
- In a medium bowl, whisk eggs, salt, & pepper until well combined.
- Spray a muffin pan very well with cooking spray, or line with silicone or parchment liners. Divide the red pepper, onion, ham/bacon/sausage, and cheese over 12 wells.
- Pour the egg mixture over the cheese mixture.
- Bake for 22-25 minutes or until set.
- Let rest 3 minutes. Run a butter knife along the edges to release the muffins and remove them from the muffin tin.
- Serve warm or let cool completely and refrigerate or freeze.
Video
Notes
Nutrition Information
Nutrition information provided is an estimate and will vary based on cooking methods and brands of ingredients used.
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I made these Egg Muffins for the January Cooking Challenge using half sausage and half bacon in each. I also added a slice of mushroom to each. They are delicious. Thanks for the recipe.
So happy you enjoyed them! Thanks for cooking with us this month.
Super easy and fun to have breakfast for dinner. I did a variety as my youngest only likes cheese and sausage!
Another great recipe! I fried up some diced kielbasa, green pepper and green onion. I sprayed a silicone mold then placed kielbasa mixture in the molds. I added the shredded cheese. Used only 4 eggs because I used a silicone doughnut mold that makes 6. Added 1 T sour cream to the beaten eggs. I didn’t want to use my oven for the small tray, so I used my air fryer @ 325 degrees. Made a mistake by filling molds with egg mixture before placing in air fryer, making a mess. Next time will add eggs with the silicone mold already placed in the air fryer. These were the perfect size for English muffin egg omelet sandwiches. Thank you for sharing your recipes.
These are delicious !
I used homemade breakfast sausage. Just the right zest to them.
Word of advice…..if you are using a Silicone cupcake holder, put it on a cookie sheet first. Those eggs run everywhere if you try to lift it before putting them in the oven.
Made these for the first time yesterday and everyone loved them. Wondering if I could make them with a whole yolk and if so, will I need to increase the bake time?
I do these baked eggs with a whole yolk and they’re great so I’m sure you could add the other ingredients under the egg. Let us know how it goes!
Thank you Holly! Love your recipes as always!
These are delicious and a good size, much larger than the bite sized ones at Starbucks and a lot easier on the pocket book. Next time I would mix the add-ins (in the individual muffin cups) prior to adding the egg mixture. In my repeat recipe file!
loved these egg muffins! So handy on the run. I will be making these weekly! passing recipe on to friends and family. Thank you
Heynow!! Can I make these in regular size muffin pan! And if so, can I use cupcake paper liners instead of oil?
Yes you can use a regular sized muffin pan. I do find they sometimes stick to paper liners, if you have parchment liners (or squares of parchment paper pressed into each well) that works a bit better.
These are ok, but definitely not 5 stars. It’s eggs and cheese baked in a muffin tin. That’s it. I sprayed the muffin tin and used a non-stick muffin pan, but the eggs still stuck to the sides. These also didn’t get very “fluffy.” Kind of the consistency of a dense fried egg with cheese.
Oh no, I am sorry that happened Susan! I hope you still enjoyed them.
I made these for a holiday brunch and they were a hit! Super easy to make. I made 24 (actually 26) mini muffins and it was perfect.
made these today in my second batch I added maple syrup everyone loved them
Happy (belated) Birthday, Holly! I have so many of your recipes bookmarked and I make them more often than not. You are my “go to” for recipes…always SO good and between my Instant Pot and slow cooker, I have to keep my cook stove dusted off.
I’m making these egg muffins tonight since I’m just getting into prepping more often. Walking up to 12,000 steps a day to get these 20 pounds off since I retired in February…boy, it’s not easy to do!
Thank you for all your delicious, easy recipes!
Thank you so much, Susie! So glad you are enjoying our recipes ❤️
Hi Holly!
Just popping in to wish you a VERY Happy Birthday! (a little birdie may have mentioned it on her blog this morning )
I hope your day is magical, and filled with family, friends, love, laughter, and PRESENTS. Don’t forget the presents! And that someone else honors you by preparing the food, and CAKE! Lots of each.
Blessings, & best wishes, from Alberta, Canada
Thank you so much for your well wishes Terry! :) It certainly was a perfect day filled with so much love!
I have made these Egg Muffins 3 times now and changed up the ingredients each time, using a different meat selection or combination. I have also added mushrooms. They keep in the freezer until ready to use, then I use the microwave to reheat. Turns out perfect every time, easy and delicious.
Easy and delicious, also versatile! Thank you!!!
How should you store these for later use?
Hi Laura, you can find all of this information in the post right above the recipe.
This egg muffin recipe will keep in the fridge for up to 5 days in an airtight container. If you’d like to keep them longer, I would suggest freezing your egg muffins. We place them in a freezer bag and lay them flat until frozen. To reheat egg muffins, simply microwave them for about 30-60 seconds or so from the fridge. If they’re frozen, they’ll need a bit longer, about 60-90 seconds.
I hope this helps!
Hello,
I just finished making these egg muffins for the second time and I can’t figure out what I am doing wrong. They are a bit gnarled looking and some will rise up evenly but most will rise on one side, lean over and then when taken out to cool they relax but in no way look like a muffin shape like your pictures. They taste good but look ugly. Could it be my oven? Somebody help! :)
I haven’t had this issue so I can’t say for sure Cheryl. It could be your oven. Are you cooking them on convection? It could also because you are overfilling your muffin tins. I hope this helps.
In the past, I had a kitchen only because my home came with one. :) But after seeing your recipes and making a couple easy dishes I am more confident. I was intimidated by spices and which ones to use, timing on the oven etc. You’ve made it so easy that now I’m looking for something to make almost every weekend for the next work week. The Egg Muffins are so good. Tomorrow I’m doing the Greek Dressing (in my Blendjet) for my Tortellini salad. I can’t believe I am excited to be in the kitchen. :) You’re the best and thank you Holly.
Kind Regards,
Anne
You just made my day Anne! Thank you for sharing your kind words and I am so glad I can help you enjoy being in the kitchen!
I totally agree. This site has made all the difference. Everything is so good and the instructions and tips are crystal clear.
These were good right out of the oven, but I didnt care for them the next day- rewarmed.
I’m single / live alone but love to cook & bake. Congratulations on Spend w/ Pennies. I have a gut strong feeling I’m going to enjoy this site …. looking forward to start my “Make Ahead Egg Muffins” … they look delicious not to mention for me, cooking is therapeutic and fun. Once again; Kudos!
I also will be the only one eating my egg muffins, Eddie. I made them for the first time today and they were delicious, minus the cheese……….because I forgot to add it. However there appeared a little concave in the center after cooked and I just added it then and it melted nicely while they were cooling. I hope you had a chance to make them. they are so good with bacon bits added in the mix.