Mini Frittata Egg Muffins

Whether you’re in need of new meal prep recipes, looking for easy ways to sneak in extra veggies, or just love egg recipes, these Mini Frittata Egg Muffins are just what you need! Made with simple, nourishing, gluten-free ingredients, they’re a quick protein-packed breakfast, brunch, or snack you can feel good about! Dairy Free and Vegetarian Options. 

Three Fritatta Muffins being stacked on one another.

What Are Mini Frittata Egg Muffins? 

If you’ve never had egg muffins or egg muffin cups before, prepare for your whole life to be changed. Okay, that might be a bit dramatic, but they’re pretty great! Or, we think so, at least. Simply put, egg muffins are just what they sound like – eggs baked in a muffin tin.

Cooked Frittata Muffins in a muffin pan.

However, we took them one step further with a frittata-style spin. Essentially, we added all our favorite frittata and omelet mix-ins, baked them in the oven, and voila! Fluffy, delicious, gluten-free egg muffins for the win! 

Brunch-Inspired Ingredients and Substitutions

It’s no secret we love a good brunch recipe. After all, with options like Brunch Charcuterie Boards, Vegan Buckwheat Banana Waffles, and our Baked Vegan Donut Recipe, who can resist a good spread?! Not us! And these mini frittata egg muffins are the perfect contribution to your morning lineup. Not only are they completely delicious, but they also allow for an easy way to sneak in extra nutrients and veggies so you can start your day off on the right foot! Here’s everything you’ll need: 

Frittata egg base in a glass bowl being held by hands.
Red onions, bacon, cheese, hot sauce, red pepper, spinach, and arugula separated and ready to be added to frittatas.
  • Eggs and Egg Whites – This combination forms the base of our egg muffins, providing flavor, texture, healthy fats, and protein. Plus, the extra egg whites make them extra fluffy. 
  • Hot Sauce – Used to add tons of flavor and just a hint of spice. 
  • Spices – Salt, black pepper, and garlic powder are all you’ll need.
  • Veggies – Onion, bell pepper, spinach or arugula, and potatoes combine for extra color, texture, and nutrients. The best part? The flavor is so tasty, your picky eaters won’t even realize they’re eating their veggies! 
  • Cheese – We used Feta cheese, but Cotija cheese or anything else you have on hand tastes great, too. 

Dairy-Free Swap: To make these egg muffins dairy-free, swap out the cheese with your favorite dairy-free variety. Or, omit it completely. 

  • Protein – Technically optional, we love to include sliced smoked salmon, chopped cooked bacon, or even leftover chicken for added protein. 

Flavor Variations

One of the best things about this egg muffin recipe is that it’s completely customizable to fit your needs and preferences. Plus, it’s a great way to use up any leftovers you have on hand! For instance, try out some more of our favorite flavor variations: 

  • Mediterranean: Include grape tomatoes, baby spinach, red onions, roasted red peppers, and a sprinkle of feta cheese. 
  • BLT: Mix in cooked bacon, spinach, and tomatoes. 
  • Pizza: Use your favorite pizza sauce, mozzarella cheese, basil, oregano, and pepperoni or sausage. 
  • Ham and Cheese: Dice up cooked ham and combine it with sharp Cheddar cheese or a dairy-free cheese sauce
Pro Tip

Note: As long as you follow the instructions to create the base, you can easily mix and match whatever add-ins you like best. You really can’t go wrong with this egg muffin recipe! 

How to Make The Best Mini Frittata Egg Muffin Cups

This egg muffin recipe gives you all the flavor of your favorite breakfast frittata but is way quicker and much easier to make! 

  1. Prepare. Preheat your oven, and generously grease or line a muffin tin. 
  2. Form the Base. In a large bowl, whisk the eggs and egg whites together until smooth. Add the sauce and spices, and stir again.
Egg base in a glass bowl and assorted ingredients on a cutting board.
Muffin pan full of frittata egg base.
  1. Fill the Pan. Fill each muffin cup halfway up with the egg mixture. Then, sprinkle the veggies and cheese on top. Spoon the remaining egg mixture on top followed by your protein and more cheese, if using. 
Egg base topped with veggie in a muffin pan.
Egg base topped with veggie in a muffin pan and ready to go in the oven.
Cooked Frittata Muffins in a muffin pan.
  1. Bake. Place the egg cups in the oven until the eggs are set and the “muffins” are brown around the edges. A toothpick should come out clean when inserted into the center.
  1. Cool. Allow the egg muffins to cool slightly in the pan before transferring them to a wire rack to finish cooling completely. 

Tips to Prevent Your Egg Muffins from Sticking

Egg Muffins are notorious for sticking to the pan. So, it’s crucial to follow the tips below. Otherwise, they’re likely to stick, crumble, and fall apart! 

Close up of Frittata Muffins in muffin pan.
  • Use an Oil Spray. Be sure to liberally spray your muffin pan, coating every nook and cranny with your favorite oil spray (Oil or butter would work, too). Then, go ahead and spray it again for good measure! Seriously. It’s that important. 
  • Opt for a Silicone Muffin Pan. If you’ve never tested out a silicone pan before, now is the time! They work like a charm to prevent foods from sticking and are super easy to clean up. 
  • Use Muffin Liners. Muffin liners and parchment paper baking cups are also useful to provide a barrier between the muffins and the pan. 

Storage Options

When it comes to batch cooking and gluten-free meal prep, these egg muffin cups are a staple in our recipe arsenal. Quick and easy, they store well and keep for days for quick breakfasts, lunches, and more! 

Refrigerator: Once cooled, these egg muffins can be transferred to an airtight container or sealable bag and stored in the fridge for up to 3 days. They’re perfect for packing in lunchboxes, and taking on the go! 

Freezer: Wrap each cooled muffin in plastic wrap, and transfer them to a sealable bag where they can be frozen for up to 3 months

To Enjoy: To reheat, let your muffins thaw in the fridge overnight. Or, warm them up straight from the freezer! If thawed, they should heat quickly in intervals of 30 seconds. From frozen, they’ll take 1-2 minutes to thaw and warm completely. 

Side view of a cooked Frittata Muffin.

Egg Muffins: Common Questions

Why is my egg muffin recipe soggy? 

If your recipe turns out soggy, it’s most likely due to excess moisture from the veggies. The best way to prevent this from happening is to give them a quick sauté before adding them to the muffin cups. 

Why are my egg muffins hollow? 

It is natural for egg muffins to deflate a bit as they cool. However, if you find your recipe is completely falling flat, it’s most often due to overbeating the eggs. Be sure to whisk them together just until combined. 

Do egg muffin cups need to be refrigerated? 

Yes, unlike regular muffins, egg muffins must be refrigerated to prevent the eggs and dairy from spoiling. 


More of Our Favorite

Gluten-Free Egg Breakfast Ideas

Looking for more gluten-free egg-filled breakfast and brunch recipes? Check out some of our favorites below! 

Three Fritatta Muffins being stacked on one another.

Mini Frittata Egg Muffins Recipe

  • Author: Lindsay Cotter
  • Total Time: 40 minutes
  • Yield: 11-12 muffins
  • Diet: Gluten Free


Whether you’re in need of new meal prep recipes, looking for easy ways to sneak in extra veggies, or just love egg recipes, these Mini Frittata Egg Muffins are just what you need! Dairy-Free and Vegetarian Options.


  • 10 large eggs
  • 2 large egg whites or equivalent liquid egg substitute
  • 2 to 3 Tablespoons picante or other hot sauce
  • ¼ teaspoon kosher salt
  • ¼ teaspoon black pepper
  • ¼ teaspoon garlic powder, optional
  • 3 Tablespoons diced red or white onion
  • ½ medium bell pepper, thinly sliced or ¼ cup chopped
  • ¼ to cup baby spinach or arugula
  • ¼ cup crumbled Feta cheese, cotija cheese or cheese of choice (skip for dairy free option)
  • Optional protein topping – sliced smoked salmon, cooked chopped bacon, cooked chicken sausage


  1. Preheat the oven to 350 degrees F (175 degrees C). Generously grease a 12-muffin cup pan with nonstick cooking spray or line with paper muffin liners. (See notes)


Baking Tips – To prevent the egg muffins from sticking, generously coat the muffin pan with nonstick spray or use a silicone muffin pan. 

  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American


  • Serving Size: 1 muffin
  • Calories: 81
  • Sugar: 0.7 g
  • Sodium: 218.7 mg
  • Fat: 5.1 g
  • Saturated Fat: 1.9 g
  • Carbohydrates: 1.2 g
  • Fiber: 0.2 g
  • Protein: 7 g
  • Cholesterol: 172.1 mg

Keywords: frittata, egg muffins, egg muffin recipe, eggs, breakfast, brunch, gluten-free

Do you have questions, feedback, or tips about this recipe? Leave a comment below with any questions or feedback you’d like to share!