This breakfast egg muffins recipe makes the ideal healthy meal or snack! Bake eggs in muffin cups, then refrigerate for quick meals.

Egg Muffins

Here’s a customizable make-ahead recipe that works for healthy breakfast, lunch and snack: Egg Muffins! Bake up scrambled eggs in muffin tin cups with healthy veggies, then refrigerate them for meals all week! This works as a grab-and-go breakfast, and it’s perfect for kid lunch boxes. We also find ourselves sneaking them out of the refrigerator for a quick snack. The filling is packed with good stuff: loads of spinach, cottage cheese for healthy protein, and jarred red pepper. They’re easy to whip up and so full of flavor!

Ingredients in breakfast egg muffins

Egg muffins are scrambled eggs that are baked in muffin tin cups, often with added vegetables or meat. Our spin on an egg muffin recipe loads up on healthy vegetables: spinach and red pepper. Because why not pack in healthy veggies? This makes them perfect for a healthy breakfast or lunch boxes. Our son loves these (and he’s wary of spinach: go figure!). Here’s what you’ll need:

  • Eggs
  • Oregano, garlic powder, salt and pepper
  • Frozen spinach: don’t substitute fresh; frozen spinach has a specific texture you’ll want her
  • Cottage cheese: bold, savory flavor and velvety texture and adds protein
  • Parmesan cheese
  • Jarred roasted red peppers: substitute sundried tomatoes if desired
Egg Muffin Cups

Bake the eggs in muffin cups

This egg muffin cups recipe is simple: whisk up the eggs, add the cheese and veggies, and bake it up! Head to the recipe below. But here are a few notes on the baking process:

  • Important: squeeze out as much water as possible from the spinach! The spinach should feel like dry crumbles when you are done. This makes sure the egg muffins will hold together when baking and won’t be too watery.
  • Spray or grease the muffin tin well. You’ll want to be able to pop the egg muffins right out after baking!
  • Bake until puffed and golden, 22 to 24 minutes. They’ll deflate a bit after you let them cool: that’s expected!
Healthy Egg Tin Muffins

Variations on egg muffins

These healthy breakfast egg muffins are exactly what we love in the morning: they’re packed with vegetables and healthy protein! But if you like, you can customize egg muffins to have different variations. Add ½ cup additional mix-ins to the recipe below, or remove the spinach entirely and substitute about 1 to 1 ½ cups mix-ins. Here are some ideas (make sure they are finely chopped):

Important notes: You’ll want the veggies on the done side when you sauté them, so they don’t release too much moisture while baking. They should be finely chopped for good distribution. Also, make sure to keep the cottage cheese in the base recipe; or you can replace it with milk.

Egg Muffins Recipe

Storage info

The great part about these egg muffins? They keep very well! They’re perfect for storing in the refrigerator for meals all week.

  • Store refrigerated for up to 5 days: you can eat them cold, room temp, or re-warmed. Personally we like them room temp!
  • You can also freeze them for up to 3 months. Defrost by placing in the refrigerator overnight.

Another spin: crustless quiche!

This egg muffin recipe is a spin on our Crustless Spinach Quiche. So if you prefer, you can make this recipe in a pie pan and slice into wedges. Simply bake it for 25 to 30 minutes until puffed and golden. Head to the linked recipe for more details!

Crustless Quiche

More healthy breakfast and lunch ideas

You can never have enough healthy breakfast or lunch ideas, in our opinion at least! Here are some more of our favorite resources:

This egg muffin cups recipe is…

Vegetarian and gluten-free.

Healthy Breakfast Egg Muffins
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Egg Muffins

Easy Egg Muffins

  • Author: Sonja Overhiser
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 12 1x


This breakfast egg muffins recipe makes the ideal healthy meal or snack! Bake eggs in muffin cups, then refrigerate for quick meals.


  • 10 to 12 ounces frozen spinach*
  • 6 large eggs
  • ½ teaspoon dried oregano
  • ½ teaspoon kosher salt
  • ¼ teaspoon garlic powder
  • 1 cup cottage cheese
  • ¼ cup grated Parmesan cheese
  • ¼ cup chopped roasted red pepper (from a jar), plus more for topping
  • Fresh ground black pepper


  1. Preheat oven to 375°F. Spray or grease a standard 12-cup muffin tin.
  2. Place the spinach in a colander and let warm water run over it until it is thawed, about 1 minute (some brands take a bit more effort to defrost: you can also use a microwave if necessary). Then use your hands to squeeze out as much excess liquid as you can.
  3. In a large bowl, whisk the eggs. Then stir in the oregano, salt, garlic powder, cottage cheese, grated Parmesan cheese, spinach, and roasted red pepper. Add a few grinds of fresh ground black pepper if you like.
  4. Fill each muffin cup three-quarters of the way to the top with the egg mixture. Sprinkle the tops with additional chopped roasted red pepper.
  5. Bake 22 to 24 minutes until set in the center and golden around the edges. Allow to cool for a few minutes (they’ll deflate, which is expected), and then run a butter knife around the edges of each muffin to loosen it and pop it out. Enjoy immediately or store refrigerated for up to 5 days: you can eat them cold, room temp, or re-warmed. (You can also freeze them for up to 3 months and defrost by placing in the refrigerator overnight.)


*Note: To customize the mix-ins in this recipe, substitute about 1 to 1 ½ cups mix-ins for the spinach. Try finely chopped sauteed broccoli, ham or bacon, caramelized onions, roasted peppers and onions or sautéed peppers, sauteed mushrooms, and so forth. You’ll want the veggies on the done side when you saute them, so they don’t release too much moisture while baking.

  • Category: Breakfast
  • Method: Baked
  • Cuisine: Breakfast
  • Diet: Vegetarian

Keywords: Egg muffins, egg muffins recipe, breakfast egg muffins, egg muffin cups, healthy egg muffins

About the authors

Sonja & Alex

Meet Sonja and Alex Overhiser: Husband and wife. Expert home cooks. Authors of recipes you'll want to make again and again.

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  1. Hi! I’m looking forward to trying your recipe. My daughter is vegetarian, and I’m always looking for breakfast recipes with protein for her.
    I have a question though…is there anything I can substitute for the cottage cheese? We’re not big fans. Maybe feta? Or half feta, half cottage cheese? I use both of those for a spinach soufflé that I make.

    1. If you’re ok with half cottage cheese and half feta, that would be great! You can’t really taste the cottage cheese, it really integrates into the flavor of the muffin. But we get it! I’d do a scant 1/2 teaspoon on the kosher salt to account for the saltier cheese. Good luck!

  2. Is there a certain way you suggest warming these up? I’m making 24 ahead of time and will need to reheat them all (ideally, quickly) 2 days later to take to a group meeting.

    1. Great question! Will you have time to throw them in the oven? Store them refrigerated and then try reheating by placing in a single layer on baking trays and bake in a 375 degree oven for about 15 minutes.