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 on a white plate

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.
ham , onion , pepper , eggs , cheese and salt and pepper with labels to make Make Ahead Egg Muffins

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.

  1. Grease the muffin tin well or use silicone liners.
  2. Add the add-ins to the muffin wells and top with beaten egg.
  3. 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!

plated Make Ahead Egg Muffins
4.96 from 163 votes↑ Click stars to rate now!
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Make Ahead Egg Muffins

Egg muffins are a delicious and tasty breakfast, naturally low carb, and easy to make ahead of time!
Prep Time 10 minutes
Cook Time 22 minutes
Total Time 32 minutes
Servings 12 servings


  • 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


  • 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.



Eggs: Muffin tins can vary in size slightly (and it can also depend on how much “add-ins” are added) so you may need a little bit more or less egg, fill the wells about ¾ full or a little bit more. I use 10 eggs to make 12 muffins. They will puff up as they bake and fall a bit after baking.
This recipe can also be made using 6 whole eggs and 1 cup of egg whites. 
Additions: Add any kind of leftovers, potatoes, veggies, or meats. If you add extra add-ins, you may need a bit less egg.
If using sausage, cook in a large skillet over medium-high heat until no pink remains.
Reheating: Reheat cooked egg muffins in the microwave for 30-60 seconds or until heated through.
4.96 from 163 votes

Nutrition Information

Serving: 1egg muffin | Calories: 128 | Carbohydrates: 1g | Protein: 11g | Fat: 9g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.01g | Cholesterol: 158mg | Sodium: 379mg | Potassium: 77mg | Fiber: 0.2g | Sugar: 1g | Vitamin A: 495IU | Vitamin C: 7mg | Calcium: 122mg | Iron: 1mg

Nutrition information provided is an estimate and will vary based on cooking methods and brands of ingredients used.

Course Breakfast, Snack
Cuisine American
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Make Ahead Egg Muffins with a bite taken out with writing
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Holly is a wine and cheese lover, recipe creator, shopping enthusiast and self appointed foodie. Her greatest passion is creating in the kitchen and making deliciously comforting recipes for the everyday home cook!
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Recipe Rating


  1. I have an oversized silicone muffin pan by Trudeau, and this was my first attempt at these bad boys. I used both a small red and an anaheim pepper and seasoned the turkey sausage and onion in a skillet with salt, garlic powder, and paprika. Then mixed the peppers and meat/onion with a handful of cheese and added some thick Tillamook slices on top at the end. Also, I used the whole eggs option. Absolutely delicious for now, and I hope they’re just as good when reheated in the morning! This site has been my go-to for the best chili ever and now I have another fave so thank you!!5 stars

  2. This recipe is sooooo good and easy to do. I loved it and so my family. I will make it again and again. Thank you so much!5 stars

  3. Great recipe! With my old muffin tins, a recipe makes closer to 18 muffins. I always make it exactly by the recipe the first time, and I enjoyed it very much. I did use some leftover green bell pepper, so mine look like Christmas treats!

    I like a little spice in my muffins, so I’ll start experimenting with spices the next go-round. All of that said — this is a great recipe for someone on the go who needs something they can wrap in foil and eat on the way to somewhere! They were easy to make, nutritious and tasty, too!5 stars

  4. I made these with the 12 whole eggs. Turned out really good. The only thing is there was too much for the cups.5 stars

  5. I don’t see 1 cup of egg whites in the recipe. How many whole eggs would you use if you included the egg whites please.

    1. Hi Camille, we use 12 whole eggs for this recipe (yolk and whites). Hope that helps!

  6. These were so easy and delicious! My husband loves them and wants me to make more. The first batch, I didn’t grease the muffin pans enough and overfilled so they stuck a bit but not much. The second batch I over greased the pan and didn’t fill as much and they turned out perfect! Highly recommend and can’t wait to try out different filings.5 stars

  7. Could these be made in a mini muffin pan? My bridal shower is in 2 weeks and it’s a tea theme song I’m looking for one bite options!

    1. Definitely! You will want to reduce the cooking time so they don’t end up rubbery but I think that sounds like such a fun idea! Congratulations on your upcoming wedding Megan ♥️

  8. Can you make the crustless egg cups in a pie pan like a quiche? I’m preparing for a bridal brunch and thought this would be excellent for those who are gluten free.5 stars

  9. So…my eggs cups ran all over the place and sunk in the middle and stuck to the muffin tin to the point I will throw it out. I did a few in silicone molds without the cheese and those ones worked perfectly. Not sure what happened with the others?!2 stars

    1. I’d think that you didn’t grease the muffin tin well enough and also overfilled them.

  10. Super easy to make and very tasty….. I served mine up between a toasted English muffin…….. perfect start to a new day 5 stars

    1. I prefer greasing my muffin tin but you can use cupcake papers. The egg mixture will stick a little to the wrapper but it will stick work :)

  11. After making these several times, this weekend’s batch was the 1st time I had extra. I found that the ones in the fridge were soggy the next day.
    Has anyone else encountered this? Any suggestions?5 stars

    1. Sorry to hear that happened. I have not had that problem when storing leftovers. Before placing them in the fridge make sure they are completely cooled and store them in an airtight container. Hope that helps!

  12. This is a fantastic recipe as written. It is so quick and easy and from reading the reviews it’s obvious you can customize it to your taste. There are no out of the ordinary ingredients.
    I’ve been making these for three weeks they freeze perfectly, they are wonderful.
    If someone in your world some sort of carb, I suspect it would be equally as good between to English muffin halves.5 stars

  13. I do lots of cooking and am constantly on the alert for simple, tasty recipes. However, most recipes call for ingredients not normally on hand at home or overly complex. It’s a real boon to find simple, delicious recipes that can easily be made from products that you routinely have on hand. I particularly like to avoid recipes that call for pre-prepared ingredients, since they are typically high in sodium, fat and sugar. These recipes and simple, tasty and amazing. This will become my new GO TO recipe source for a quick, healthy, hearty meal.

    1. I don’t’ have any experience with a baby cakes machine so I can’t say for sure. I would suggest you consult the product manual. Let us know how it goes!

      1. Made these for my husband for the morning protein. He loved them and he is pretty picky. I used left over taco meat. He is also trying to lose weight and kick the fast food eating on the run.5 stars

  14. I used Jimmy Dean Sage sausage. I lightly sauteed the onions/peppers with the meat. I only did half the recipe and had 4 eggs so used 1 c milk & 1 slice wholegrain sourdough for additional filler. Also used grease from sausage to moisten the tins. Not a fan of cooking spray. Worked perfectly!5 stars