A variety of breakfast egg muffins sit on a gray background.

I know you guys love Overnight Oats when it comes to meal prep breakfasts (and I really like them, too), but my absolute favorite meal prep breakfast? EGG CUPS! AKA: egg muffins, baked eggs, or egg muffin cups.

These grab-and-go bite-sized breakfast muffins are easy to make, packed full of nutrition and flavor, and totally customizable—we’re giving you four flavors to try out in this post, but you can let your imagination run wild! There is just so much robust flavor in the savory breakfast world—and these egg muffins explore that with flavors like Turkey Spinach, Sweet Potato Chive, Ham and Cheddar, and Caprese!

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Four varieties of egg cups are uncooked in a muffin tin.

How do you make baked egg muffins?

Meal prepping egg cups is as simple as spraying a muffin tin with cooking spray (or using silicone baking cups), and then layering the ingredients in the recipe in each cup. Then you bake it in 350°F oven until you reach the desired egg yolk consistency (10-12 minutes for a soft yolk, 12-15 minutes for a hard yolk). All of these egg muffin flavors bake for the same amount of time, so you can mix and match flavors in the same batch without any troubles.

Why should you make breakfast egg cups?

I like making these egg cups because they make breakfast (and snacks!) so super simple! They take just a few minutes to prep and cook, and then you have an easy grab-and-go breakfast all week long. And if you’re someone like me who prefers savory foods in the morning, this is a great alternative to classic meal prep breakfasts like overnight oats.

Three egg muffins are stacked on a gray countertop.

Can you freeze these?

I know some people freeze egg muffins, but I personally find that the freezer changes the texture of the egg enough that I never do. If you want to try it, arrange the cooked egg muffins on a piece of parchment or a silicone baking mat on a baking sheet. Freeze flat until frozen solid. Transfer to a glass food storage container or zip-top freezer bag, label, and keep frozen for up to three months.

How long do these muffin cups last in the fridge?

These cups will last for 3-7 days in the fridge, depending on which flavor you choose. I personally wouldn’t want the Spinach Egg Cup kicking around for more than three days because I have some serious texture issues with older, cooked spinach (slimy—blech). But the Ham and Egg Cups with Cheddar could probably hang out in the fridge for up to a week without issue (I say “probably” because our family can plow through egg cups like they’re going out of style—so they’ve never actually stayed around a full week).

Three turkey spinach egg cups are stacked.

Can you eat them cold?

I tend to eat my egg cups cold, straight out of the fridge. My personal preference is to cook them to the hard yolk stage (12-15 minutes) for cold eating—just like eating a hard-boiled egg.

How do you reheat these?

If you’re not feeling eating your egg muffins cold, they also warm up beautifully in the toaster oven or conventional oven. Just pop them in a 350°F oven for 5-10 minutes until warmed through. I do not recommend reheating them in the microwave—at best, the egg tends to turn rubbery, and at worst, you might have an egg-splosion you have to clean up!

How do you keep breakfast egg cups from collapsing?

Sometimes when you bake eggs, they end up deflating after cooling—that problem happens much more frequently with scrambled/beaten eggs than whole eggs because of how they puff up in the oven (what goes up, must come down!). Here, we use whole, unbeaten eggs, and that avoids the problem of deflating egg cups almost entirely.

Four stacks of egg muffin cups rest on a grey background. The front stack is topped with chopped herbs.

How do you make vegetarian egg cups?

Two of our flavors below—Caprese and Sweet Potato Chive—are great vegetarian options! You can also make our vegetarian version of the Spinach Egg Cups!

What’s the best way to get egg cups out of the pan?

If you’ve ever forgotten to oil a skillet before making scrambled eggs, you know just how sticky eggs can be! To make removing the egg muffins from the pan easy, here are our tips:

  • Spray each muffin cup liberally—and we mean liberally!—with oil.
  • Silicone baking cups really help. You can pop the egg muffins out of the silicone muffin cups much more easily.
  • Running a sharp knife along the side of each muffin cup can help release it from the tin—we do not recommend doing this with nonstick-coated tins because the knife can damage the coating. Instead, try a plastic or rubber spatula.
Three egg muffins are stacked on a gray countertop.

What are the best egg muffin flavors?

Let’s dig into the four I have ready for you:

  • Caprese—My favorite of the bunch! These Caprese Egg Cups have a bottom layer of chopped sundried tomatoes and lots of gooey, melty, fresh mozzarella cheese. They are finished off with some fresh basil. Yum!
  • Ham and Cheddar—A classic and simple combo that’s hard to beat! Pick up honey-glazed ham for a nice sweet undercurrent of flavor.
  • Sweet Potato Chive—These dairy-free egg muffins feature a shredded sweet potato crust topped with brightly-flavored fresh chives.
  • Spinach—I love giving myself a little burst of greens in the morning—it seems like such a nice way to kick off a healthy day!
Split image of four flavors of egg muffins, each labeled with their flavor.

What other flavor combinations can you try?

These flavor combos are just my suggestions—egg cups are really hard to mess up. I urge you to whip out your muffin tin, grab a dozen eggs, and start experimenting! Some ideas I have but haven’t tried yet: pizza egg cups, maple bacon egg cups, crash hot potato egg cups, leftover pasta egg cups (like this frittata)—the possibilities are (almost) endless! Enjoy.

Our protips for GREAT baked egg muffin cups:

  • Spray your muffin tin liberally with cooking spray to get them to release easily.
  • Reheat in the toaster oven or conventional oven instead of the microwave to avoid rubbery eggs.
  • Experiment with the flavors that you love the best!

Want more meal prep recipes like this one?

  • Vegan Blueberry Muffins. Stash these tender muffins in the freezer for easy grab-and-go breakfasts.
  • Meal Prep Breakfast Sandwiches. Start your day off right with these veggie, bacon, egg, and cheese sandwiches.
  • No-Fail Salad in a Jar Recipes. Learn how to make mason jar salads and why they are one of our favorite lunch meal preps. Then, get over a dozen salad in a jar recipes, all in one place!
A variety of breakfast egg muffins sit on a gray background.

Egg Muffins

Yield: 6 egg cups
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes

Meal prep your breakfast with these easy egg cups that come in 4 different flavors: Spinach, Sweet Potato Chive, Ham and Cheddar, and Caprese!

Note: The Turkey Spinach and Sweet Potato Chive flavors are paleo.


For Sweet Potato Chive Egg Cups

  • Cooking spray
  • 1 small sweet potato
  • 6 eggs
  • 2 tablespoons chopped fresh chives
  • 1/2 teaspoon sea salt
  • 1/2 teaspoon black pepper
  • 1/4 teaspoon garlic powder

For Caprese Egg Cups

  • 1 cup sundried tomatoes
  • Boiling water
  • 6 eggs
  • 6 ounces fresh mozzarella, chopped (or use pearl-size balls)
  • 1/2 teaspoon sea salt
  • 1/2 teaspoon black pepper
  • 1/4 teaspoon garlic powder
  • 1/2 cup chopped fresh basil


For Sweet Potato Chive Egg Cups

  1. Preheat oven to 350°F. Liberally spray six cups of a regular size muffin tin with cooking spray.
  2. Using the large holes in a box grater, grate the entire sweet potato (you should get about 1 1/2 cups of grated sweet potato). Scoop 1/4 cup of grated sweet potato into the bottom of each greased muffin cup. Press down to form a crust.
  3. Carefully break an egg into each cup. Evenly divide the chives over top of each cup.
  4. In a small bowl, mix together the salt, pepper, and garlic powder. Sprinkle evenly over the egg cups.
  5. Bake in preheated oven for 10-12 minutes (for a soft yolk), or 12-15 minutes (for a hard yolk). Let cool for 10 minutes in the muffin tin, then use a knife to loosen the sides of the cups and lift them out with a spoon.

For Caprese Egg Cups

  1. Preheat oven to 350°F. Liberally spray six cups of a regular size muffin tin with cooking spray. Set aside.
  2. If using dried tomatoes: Place the sundried tomatoes in a small bowl and cover with boiling water to reconstitute. Set aside for 10 minutes, then drain, squeeze out excess water with a clean kitchen towel, and chop roughly.
  3. If using oil-packed tomatoes: Drain from oil and chop roughly.
  4. Divide the sundried tomatoes between the six greased muffin cups.
  5. Carefully break an egg into each cup. Then top with 1 ounce of fresh mozzarella each.
  6. In a small bowl, mix together the salt, pepper, and garlic powder. Sprinkle evenly over the egg cups.
  7. Bake in preheated oven for 10-12 minutes (for a soft yolk), or 12-15 minutes (for a hard yolk). Let cool for 10 minutes in the muffin tin, then use a knife to loosen the sides of the cups and lift them out with a spoon. Sprinkle cups immediately with fresh basil.


Check out these other egg cup flavors: Spinach Egg Cups, Ham Egg Cups with Cheddar

Nutrition Information:
Yield: 12 Serving Size: 1 egg cup
Amount Per Serving: Calories: 124Total Fat: 8gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 4gCholesterol: 195mgSodium: 327mgCarbohydrates: 4gFiber: 1gSugar: 2gProtein: 10g

At Wholefully, we believe that good nutrition is about much more than just the numbers on the nutrition facts panel. Please use the above information as only a small part of what helps you decide what foods are nourishing for you.

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  1. Have you tried lining the muffin tins with paper and then spraying those with cooking spray? I’m thinking that would make clean-up easier. Do you think that would work? Thanks!

  2. How long could could lease last in the refrigerator? Also reheating them? I would like to use them for my mid morning snack.

    1. They should be good for 3-7 days, depending on the flavor. You can eat them cold, or warm them in a toaster oven.

  3. I’ve recently stumbled on your site and started with the overnight oats for my fiancee who can’t seem to eat enough to feel proper during the day…so I’ve made him overnight oats a couple times now, have an instant oatmeal ‘bag’ ready for him to pour in to a bowl and take to work tomorrow, and am loving the egg cup idea. Just made a recipe tonight that…maybe came from your site? Cheesy cauliflower egg cups for my 4 year old who WILL NOT EAT VEGETABLES. And most of the time won’t even drink smoothies. Oy. Anyway. Long story short – if I make soft yolk egg cups, how well do they reheat and does the yolk stay soft? I personally prefer a more runny egg. Thanks so much for all the info and detailed instruction!

  4. Hi Cassie! Do you think you could freeze these and reheat them from frozen in the morning? I’ve got a batch in the oven now and was curious!

    1. I’ve never frozen them, but eggs can be a bit tricky coming out of the freezer. I’d try one before you put the whole batch in the freezer. 🙂

  5. thank you for all of these recipes, great idea for prepping ahead, especially since I eat eggs every morning as part of my diet, nice time saver! Love making these in the muffin tins! Already love sweet potato, so you had me there!

  6. Mhmmmm! These looks delish! I could never figure out to get these guys to be not-super-duper-dry-overdone, so I’m looking forward to giving your directions a try! 🙂

  7. I’m 4 months pregnant and find myself really struggling with getting enough protein in an on the go breakfast to keep me full. Plus I’ve been craving sweet potatoes like woah. I can already tell these sweet potato egg cups are going to be my new jam! Thanks!

  8. I love your herbed goat cheese egg cups and they are often on my meal prep list so I can’t wait to try out some new flavours, especially the caprese one!