Meal Prep Breakfast Egg Muffin Cups: 4 Recipes to Try!

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!

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.

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).

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.

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.

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!

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!