High-Protein Pepperoni Breakfast Cups

Featured in: Forest-Style Comfort Bakes

These savory breakfast cups combine eggs with Greek yogurt for extra protein, loaded with pepperoni, mozzarella, and classic pizza flavors. Baked in a muffin tin, they're perfectly portioned for busy mornings. Each cup delivers 11 grams of protein with only 2 grams of carbs, making them ideal for high-protein, low-carb eating. The mini pepperoni and red bell pepper create that irresistible pizza taste everyone loves.

Updated on Mon, 09 Feb 2026 15:49:00 GMT
Golden-brown High-Protein Pepperoni Breakfast Cups with melted mozzarella and diced red bell peppers, fresh from the oven. Save
Golden-brown High-Protein Pepperoni Breakfast Cups with melted mozzarella and diced red bell peppers, fresh from the oven. | cocoaferns.com

Last Tuesday morning, I was staring at my fridge wondering how to make breakfast interesting when my daughter mentioned she wanted something that tasted like pizza but actually had protein in it. That's when these breakfast cups clicked into place, and honestly, they've become our go-to for those mornings when we need to eat something substantial but can't sit down for twenty minutes. The kitchen smelled incredible while they baked, and watching her face light up when she bit into one made the whole thing worth it.

I brought these to a weekend brunch gathering, and they disappeared faster than anything else on the table, which felt like a small victory since everyone was expecting some elaborate quiche situation. My neighbor actually asked for the recipe right there, and when I told her it only takes fifteen minutes of prep, she looked genuinely shocked that something this good could be that simple.

Ingredients

  • Large eggs (6): These are the foundation, and using large ones matters because size affects how the egg mixture sets and distributes through the cups.
  • Plain Greek yogurt (1/2 cup): This is the secret weapon that adds protein and keeps everything creamy without making it watery like regular milk would.
  • Milk (1/4 cup): Just enough to loosen the mixture so it flows around your fillings evenly without getting too thin.
  • Salt and black pepper (1/4 tsp each): The fundamentals that make everything taste like itself.
  • Dried oregano and basil (1/2 tsp each): These dried herbs give you that unmistakable pizza flavor without overpowering things or adding moisture.
  • Shredded mozzarella cheese (3/4 cup): Use the good stuff if you can, because it melts like a dream and actually tastes like cheese, not plastic.
  • Mini pepperoni slices (1/2 cup): Regular pepperoni works fine too if you chop it, but the mini ones distribute better and cook more evenly.
  • Red bell pepper, finely diced (1/4 cup): This adds color, sweetness, and texture without changing the flavor profile of the pizza vibe.
  • Red onion, finely diced (2 tbsp): Keep the pieces small so they cook through in the twenty minutes and give you little bursts of sharpness.
  • Grated Parmesan cheese (2 tbsp): A small amount goes a long way here, adding that salty depth that makes people wonder what the secret ingredient is.
  • Pizza sauce (2 tbsp): Choose one you actually enjoy eating straight from the jar, because that's honestly the best way to test if it's worth using.

Instructions

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Get your oven ready:
Preheat to 375°F and grease your muffin tin or slip silicone liners in there. This step feels basic but matters because it prevents your cups from sticking and makes cleanup something you won't dread.
Whisk your egg base:
Combine eggs, Greek yogurt, milk, salt, pepper, oregano, and basil in a bowl and whisk it until everything looks smooth and uniform. You're looking for the Greek yogurt to blend completely so you don't get weird lumpy bits in your finished cups.
Mix your fillings:
In another bowl, toss together mozzarella, pepperoni, bell pepper, red onion, Parmesan, and pizza sauce. This is where you can get hands-on and make sure everything is evenly distributed so no single cup gets all the pepperoni while another one seems lonely.
Layer strategically:
Divide your filling mixture evenly among the six muffin cups, pressing it down slightly so it stays put when you pour the egg mixture over top. This is less about precision and more about common sense, because uneven fillings mean some cups finish cooking before others.
Pour and distribute:
Pour the egg mixture over the fillings until each cup is about three-quarters full, then use a fork to gently stir the egg and fillings together so they're mixed but not completely homogenized. Leave a tiny bit of space at the top because these puff up slightly as they bake.
Bake until golden:
Slide everything into the oven for eighteen to twenty minutes, watching until the centers are just set and the tops have a light golden color. They're done when a fork poked in the center comes out clean, not when they're bouncy or jiggly anymore.
Cool and release:
Let them sit in the tin for five minutes, which gives them time to firm up slightly so they don't break apart when you're removing them. Run a knife around the edges if they seem stuck, and they'll pop right out.
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A close-up view of High-Protein Pepperoni Breakfast Cups showing pepperoni slices and herbs inside muffin tins. Save
A close-up view of High-Protein Pepperoni Breakfast Cups showing pepperoni slices and herbs inside muffin tins. | cocoaferns.com

There's something special about pulling warm breakfast cups out of the oven on a weekday morning and knowing you're actually eating something with substance, something that tastes indulgent even though it's technically the responsible choice. My son now requests these instead of cereal, which might be my greatest parenting achievement yet.

Make Them Your Way

The beauty of these cups is that they're infinitely customizable depending on what you have on hand or what your taste buds are craving. Swap mozzarella for provolone or sharp cheddar if you want a completely different flavor direction, or skip the pepperoni entirely and load them with sautéed spinach and mushrooms for a vegetarian version that's equally satisfying. I've even tried adding sun-dried tomatoes and fresh basil after baking, which sounds fancy but takes literally three seconds.

Storage and Reheating

These keep beautifully in the refrigerator for up to four days, which means you can make them on Sunday and actually have grab-and-go breakfasts that aren't sad string cheese and a handful of nuts. Reheat them gently in the microwave for about thirty seconds per cup, or pop them in a toaster oven at 325°F for a few minutes if you want them less steamy and more crispy on top. I've even eaten them cold straight from the fridge, which is not recommended by anyone but absolutely works in a pinch.

Why This Became a Staple

Honestly, these cups won me over because they solve the real breakfast problem, which is that most high-protein options are boring or take too long. They taste exciting, they're actually nutritious without tasting like punishment, and they fit into weekday mornings without requiring you to wake up earlier. Plus, there's something deeply satisfying about knowing exactly what went into your food and that it didn't come from some mass-produced breakfast sandwich.

  • The Greek yogurt makes them extra creamy and bumps up the protein without any weird texture.
  • Make them on your least busy day so you actually have breakfast sorted for the rest of the week.
  • Experiment with different cheeses and fillings until you find your perfect version, because the recipe is just a starting point.

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Six savory High-Protein Pepperoni Breakfast Cups served on a white plate with a small bowl of pizza sauce for dipping. Save
Six savory High-Protein Pepperoni Breakfast Cups served on a white plate with a small bowl of pizza sauce for dipping. | cocoaferns.com

These breakfast cups quietly became the thing people ask me to bring to gatherings, which is honestly the highest compliment a recipe can receive. They prove that eating well doesn't have to be complicated or boring, just thoughtful.

Recipe FAQs

Can I make these breakfast cups ahead of time?

Yes, these store beautifully in the refrigerator for up to 4 days. Reheat gently in the microwave for 30-60 seconds before serving. They're perfect for meal prep.

What can I substitute for the pepperoni?

For a vegetarian version, try sautéed mushrooms, spinach, or diced bell peppers. Cooked bacon or crumbled sausage also work well for different protein options.

Why use Greek yogurt in the egg mixture?

Greek yogurt adds extra protein and creates a creamy, tender texture. It also helps bind the ingredients while keeping the cups moist without making them heavy.

Can I freeze these breakfast cups?

Absolutely. Wrap each cooled cup individually in plastic wrap and freeze for up to 2 months. Thaw overnight in the refrigerator and reheat before serving.

Do I need to grease the muffin tin?

Yes, either grease the tin well with butter or oil, or use silicone liners for easy removal. Letting them cool for 5 minutes also helps them release cleanly.

Can I use a regular 12-cup muffin tin?

Yes, simply double the recipe to fill all 12 cups, or fill only 6 cups and leave the others empty. The baking time remains the same.

High-Protein Pepperoni Breakfast Cups

Savory muffin-tin frittatas with pepperoni and mozzarella, ready in 35 minutes

Prep Time
15 minutes
Time to Cook
20 minutes
Overall Time
35 minutes
Author: Maya Larkson

Recipe Category Forest-Style Comfort Bakes

Skill Level Easy

Cuisine Type American

Makes 2 Servings Amount

Diet Details Low Carbohydrate

What You Need

Egg Mixture

01 6 large eggs
02 1/2 cup plain Greek yogurt, unsweetened
03 1/4 cup whole milk
04 1/4 teaspoon salt
05 1/4 teaspoon black pepper
06 1/2 teaspoon dried oregano
07 1/2 teaspoon dried basil

Filling

01 3/4 cup shredded mozzarella cheese
02 1/2 cup mini pepperoni slices, or regular pepperoni chopped
03 1/4 cup red bell pepper, finely diced
04 2 tablespoons red onion, finely diced
05 2 tablespoons grated Parmesan cheese
06 2 tablespoons pizza sauce, plus extra for serving optional

Directions

Step 01

Prepare Muffin Tin: Preheat oven to 375°F. Grease a 6-cup muffin tin or line with silicone liners.

Step 02

Mix Egg Base: In a medium bowl, whisk together eggs, Greek yogurt, milk, salt, pepper, oregano, and basil until smooth and fully combined.

Step 03

Combine Filling Ingredients: In a separate bowl, combine mozzarella, pepperoni, bell pepper, red onion, Parmesan, and pizza sauce until evenly mixed.

Step 04

Distribute Filling: Evenly divide the filling mixture among the 6 muffin cups, distributing ingredients proportionally.

Step 05

Add Egg Mixture: Pour the egg mixture over the filling in each cup until about 3/4 full. Use a fork to gently stir each cup to distribute the filling throughout.

Step 06

Bake Frittatas: Bake for 18 to 20 minutes, or until the centers are just set and the tops are lightly golden brown.

Step 07

Cool and Serve: Allow to cool for 5 minutes before removing from the tin. Serve warm with additional pizza sauce if desired.

Kitchen Tools Needed

  • 6-cup muffin tin
  • Mixing bowls, medium and small
  • Whisk
  • Measuring cups and spoons
  • Fork

Allergy Info

Always check every ingredient for allergens. If you're not sure, talk to a health expert.
  • Contains eggs and dairy products
  • May contain gluten if pepperoni or pizza sauce include wheat derivatives; verify all product labels for allergen information

Nutrition Details (per portion)

Nutrition info shown is for guidance only. It cannot replace medical advice.
  • Calorie Count: 135
  • Fats: 9 g
  • Carbohydrates: 2 g
  • Proteins: 11 g