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!

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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
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  • 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.
4.97 from 181 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 Nilsson is the creator of Spend With Pennies, where she creates easy, comforting recipes made for real life. With a passion for nostalgic flavors and simplified techniques, Holly helps busy home cooks create delicious meals that always work. She is also the author of “Everyday Comfort,” which promises to inspire even more hearty, home-cooked meals.
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Recipe Rating


  1. These are very good. We reheated them in the air fryer; and, they were just as good as when we first made them.5 stars

  2. This recipe is so easy, and soooo delicious! The egg muffins come out moist and packed with the flavors of onion, bacon, red peppers, and cheese. I made a dozen and was planning on freezing half of them for another meal. No chance of that! Everyone wanted more until they were all gone!!5 stars

  3. These Egg Muffins come together so easily! I made mine with red pepper, cheddar cheese, and turkey sausage patties that I cut into bite sized pieces. These Egg Muffins are easy to eat on the go. They are such a nice alternative to a strata or quiche.5 stars

  4. I like to make egg McMuffins often so I can have a nutritious breakfast during the busy week!

    I submitted an entry for January of my version of Egg McMuffins.5 stars

  5. These muffins are very easy to make and delicious! At the time we did not have the “ham” called for so I browned breakfast sausage and crumbled….
    Thank you for the quick recipe.5 stars

  6. I just made these this morning and they are “Delicious”!! Thanks again Holly for another great recipe. I also love your banana bread ;)5 stars

  7. Kids love these… eat them like cupcakes! I did add about 1/2 cup leftover hash browns that were already cooked kinda crispy. It made a delicious crunch to an already awesome recipe. So good!5 stars

  8. My husband loved these! I added ground sausage, green onions, mini colored peppers, sage, and a little bit of yogurt in the eggs. Then followed the recipe. So good!!! ❤️5 stars

  9. Delicious!!! I made this recipe as written with ham. I made full-sized muffins. They are really really good, lots of flavor, and they bake perfectly. I have to remember this recipe next time I have company. Thanks for another extra good recipe!5 stars

    1. We loved this recipe! Even my two-year old was eating it up. I made a few plain egg muffins with just the egg, cheese, salt, and pepper. For the other ones, I added some ham, bacon, and red pepper. Delicious! I will keep it handy to make again!5 stars