Pepperoni & Cheese Pizza Protein Bagels — Baked-In Flavor

If you enjoyed my air fryer protein bagels, here’s a savory twist you’ll crave. These pizza protein bagels fold mini pepperoni, shredded mozzarella, and Italian seasoning right into the dough so every bite tastes like pepperoni pizza—no extra toppings required.

They use the same simple 2-ingredient yogurt dough and the same air fryer method, but with pizza flavor baked inside. Serve with warm pizza sauce for dipping and try not to eat them all at once.

Prep takes about 5 minutes and air frying is 16 minutes, making these ideal for meal prep, after-school snacks, or a high-protein savory breakfast that actually excites the taste buds.

Three pizza protein bagels on parchment paper served with marinara sauce and pepperoni

Why You’ll Love These Pizza Protein Bagels

  • High protein: Skyr yogurt adds protein without using protein powder.
  • Pizza flavor baked in: Mini pepperoni, mozzarella, and Italian seasoning are mixed into the dough for consistent flavor.
  • Fast prep: Mix, knead, shape, and air fry—about 5 minutes hands-on.
  • Kid-friendly: These are basically portable pizza and kids love them.
  • Meal prep friendly: Make a batch and reheat during the week for quick breakfasts or snacks.

Featured Ingredients

  • Plain skyr yogurt: Thick and high in protein; plain nonfat Greek yogurt works as a substitute.
  • Self-rising flour: Contains leavening so the bagels puff without yeast. If you only have all-purpose flour, see the FAQ for adjustments.
  • Mini pepperoni: Small pieces distribute evenly; chop regular pepperoni if needed.
  • Shredded mozzarella: Melts into the dough for gooey pockets of cheese.
  • Italian seasoning: Added to the dough and sprinkled on top for extra herb flavor.
  • Pizza sauce: Warm for dipping to complete the pizza experience.
Four pizza protein bagel dough balls with pepperoni on parchment paper
Hand shaping pizza protein bagel dough with pepperoni pieces on parchment paper
Two uncooked pizza protein bagels with seasoning in an air fryer basket
Two baked pizza protein bagels with Italian seasoning in an air fryer basket

How to Make Pizza Protein Bagels

Step 1: Mix the Dough

Preheat the air fryer to 350°F. In a large bowl combine yogurt, self-rising flour, shredded mozzarella, mini pepperoni, Italian seasoning, and sea salt. Stir with a spoon until combined, then press with your hands to form a ball.

Step 2: Knead and Shape

Turn the dough onto a floured surface and knead 1–2 minutes until smooth, adding flour as needed to prevent sticking. Divide into 4 equal portions. Roll each piece into a 5-inch log, then join the ends and pinch to form a bagel.

Step 3: Egg Wash and Season

Brush the tops and bottoms of the bagels with a whisked egg and sprinkle with additional Italian seasoning.

Step 4: Air Fry

Line the air fryer basket with parchment and place the bagels inside. Depending on your air fryer, you may need to work in two batches. Air fry 8 minutes, flip, then air fry another 8 minutes until golden brown.

Step 5: Cool and Serve

Let the bagels rest 5 minutes, then serve warm with pizza sauce for dipping.

Two hands pulling apart a pizza protein bagel to show the pepperoni inside

Tips and Variations

  • Cheese swap: Replace mozzarella with shredded Parmesan or use a blend for a different flavor profile.
  • Greek yogurt: Plain, nonfat Greek yogurt works if you don’t have skyr—avoid flavored yogurts.
  • Oven method: No air fryer? Bake at 375°F on a parchment-lined sheet for 20–22 minutes, flipping halfway.
  • Make ahead: Shape the bagels and refrigerate on a parchment-lined tray up to 24 hours before cooking; add 1–2 minutes to the cook time.
  • Storage: Keep in an airtight container in the fridge for up to 4 days. Re-crisp in the air fryer at 300°F for 3–4 minutes.
  • Extra toppings: Try a sprinkle of everything bagel seasoning along with the Italian seasoning for a fun twist.
Hand dipping a pizza protein bagel into a bowl of marinara sauce

FAQ

Can I use regular flour instead of self-rising?

Yes. For each cup of all-purpose flour, add 1½ teaspoons baking powder and ¼ teaspoon salt. If you do this, omit the extra sea salt called for in the recipe.

How much protein is in each bagel?

Each bagel contains roughly 14–16g of protein from the skyr, mozzarella, and pepperoni. Exact amounts vary with the brands you use.

Can I freeze these?

Yes. Cool completely, freeze in a single layer, then transfer to a freezer bag. Reheat from frozen in the air fryer at 325°F for 5–6 minutes.

More Protein Bagel Recipes

  • Air Fryer Protein Bagels — A simple base with everything seasoning.
  • Blueberry Crunch Protein Bagels — Sweet with a brown sugar crumble.
  • Strawberry Cottage Cheese Bagels — A cottage cheese version with fresh strawberries.
Overhead view of three baked pizza protein bagels with marinara sauce and pepperoni
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Pizza Protein Bagels

Simple 2-ingredient yogurt dough packed with mini pepperoni, mozzarella, and Italian seasoning. Air fries in under 20 minutes—serve with warm pizza sauce!
By: Lee Funke
Prep: 5 mins
Cook: 16 mins
Total: 21 mins
Servings: 4 bagels
Pizza protein bagels with Italian seasoning served with marinara sauce and pepperoni slices

Ingredients

Bagel Dough

  • 1 cup plain skyr yogurt (or plain nonfat Greek yogurt)
  • 1 cup self-rising flour, plus more for kneading
  • 1/4 teaspoon sea salt
  • 1/4 cup shredded mozzarella cheese
  • 1/4 cup mini pepperoni
  • 1 teaspoon Italian seasoning, plus more for topping

Egg Wash + Serving

  • 1 large egg, whisked
  • Pizza sauce, for dipping

Instructions

  • Preheat the air fryer to 350°F.
  • In a large bowl combine yogurt, flour, mozzarella, mini pepperoni, Italian seasoning, and sea salt. Stir until combined, then press with your hands into a ball.
  • Transfer to a floured surface and knead 1–2 minutes until smooth, adding flour if sticky.
  • Divide into 4 pieces, roll each into a 5-inch log, then join the ends to form bagels.
  • Brush tops and bottoms with egg wash and sprinkle with Italian seasoning.
  • Place on parchment in the air fryer basket (work in batches if needed). Air fry 8 minutes, flip, then air fry 8 more minutes until golden.
  • Cool 5 minutes and serve warm with pizza sauce.

Tips & Notes

  • Swap mozzarella for shredded Parmesan or use a combination for a different flavor.
  • Plain nonfat Greek yogurt is an acceptable substitute for skyr.
  • Shaped bagels can be refrigerated up to 24 hours before cooking—add 1–2 minutes to the cook time.
  • If you don’t have an air fryer, bake at 375°F for 20–22 minutes, flipping halfway.
  • Store in an airtight container in the fridge up to 4 days. Reheat in the air fryer at 300°F for 3–4 minutes.

Nutrition

Serving: 1,
Calories: 220 kcal,
Carbohydrates: 26 g,
Protein: 14 g,
Fat: 6 g,
Fiber: 1 g,
Sugar: 2 g

Nutrition information is an approximation.

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