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Pepperoni Pizza Bites

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Pepperoni Pizza Bites are like those frozen mini bagel pizzas, only made from scratch in a muffin tin using my Greek yogurt bagel dough.

Pepperoni Pizza Bites
Pepperoni Pizza Bites

My daughter loves those mini frozen bagel pizzas, so I wanted to make an easy Pepperoni Pizza Bite recipe from scratch. I figured making bagels and then topping them with pizza ingredients would take too long, so I streamlined them and made them in muffin tins instead. These mini pizza bites would be great for an afternoon snack or even a party appetizer. If your kids like these pizza bites, you should also try my Pizza Sausage Rolls and Stuffed Bagel Balls.

Pepperoni Pizza Bites

How to Make Pizza Bites

  • Make the pizza dough: Combine the dry ingredients and then add the yogurt. Knead the dough until it is tacky but not sticky. You can also use premade pizza dough to make this faster.
  • Divide the dough into 16 balls and press each into the greased muffin tin.
  • Bake the dough for 15 minutes at 375 degrees and remove it from the oven.
  • Top your pizza bites: Gently press the dough down in the middle of each cup to create a small well. Top each with sauce, mozzarella cheese, and chopped pepperoni.
  • Bake the bites for three more minutes until the cheese is melted. Carefully remove the mini pizzas from the oven and let them cool before eating.

Pizza Topping Ideas and Variations

I used turkey pepperoni on my pizza bites, but you can top them with anything you like on your pizza! Here are some ideas:

  • Veggie with finely diced bell peppers or any chopped leftover veggies
  • Caprese with fresh mozzarella and basil
  • Pesto pizza with pesto and cheese
  • White pizza with ricotta, mozzarella, and Italian seasoning
  • Dessert pizza with Nutella and mini marshmallows
  • I made homemade bagel dough so my pizza bites would have extra protein, but you can also buy pre-made pizza dough.

plate of bagel pizza bitesPepperoni Pizza Bites

More Pizza Recipes You’ll Love:

Pepperoni Pizza Bites

4.76 from 33 votes
Pepperoni Pizza Bites are like those frozen mini bagel pizzas, only made from scratch in a muffin tin using my Greek yogurt bagel dough.
Course: Appetizer, Lunch, School Lunch, Snack
Cuisine: American
Pepperoni Pizza Bites
Prep: 10 mins
Cook: 30 mins
Total: 40 mins
Yield: 4 servings
Serving Size: 4 bites


  • Olive oil spray
  • 1 cup unbleached all-purpose flour, whole wheat or gluten-free mix, (5 oz in weight)
  • 2 teaspoons baking powder, make sure it’s not expired, or it won’t rise
  • 3/4 teaspoon kosher salt, diamond crystal, use less if using table salt or Mortons
  • 1 cup non-fat Greek yogurt, not regular yogurt, it will be too sticky (I recommend Stonyfield)
  • 2/3 cup marinara or pizza sauce
  • 1 cup shredded part-skim mozzarella cheese
  • 1 ounce turkey pepperoni, chopped
  • Crushed red pepper flakes, for serving (optional)


  • Preheat oven to 375˚F and spray two 12-cup stand size muffin tins with oil.
  • In a medium bowl combine the flour, baking powder and salt and whisk well.
  • Add the yogurt and mix with a fork or spatula until well combined, it will look like small crumbles.
    how to make greek yogurt dough
  • Lightly dust flour on a work surface and remove dough from the bowl, knead the dough a few times until dough is tacky, but not sticky, about 15 turns (it should not leave dough on your hand when you pull away).
  • Divide the dough into 16 equal-size small balls (about 25 grams each).
  • Press each ball into the bottom of the muffin cups, allowing it to go up the side slightly.
    muffin tin with dough
  • Bake for 15 minutes, remove from oven and carefully press balls down in the middle to create a small well.
  • Top each ball with 2 teaspoons sauce, 1 tablespoon cheese and a sprinkle of pepperoni.
    Pepperoni Pizza muffins
  • Return to the oven and bake 3 minutes, or until cheese is melted.
  • Remove from oven and allow to cool 2 minutes.  With a paring knife or metal offset spatula, carefully remove the bites, cutting around the top to remove any cheese that may have stuck to the pan.
  • Spray the pan again and repeat with remaining dough and toppings.

Last Step:

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Serving: 4 bites, Calories: 286 kcal, Carbohydrates: 31 g, Protein: 18 g, Fat: 9.5 g, Saturated Fat: 4.5 g, Cholesterol: 30 mg, Sodium: 974 mg, Fiber: 1.5 g, Sugar: 4 g


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74 comments on “Pepperoni Pizza Bites”

  1. Delicious! My boys are 21 and 27 and they loved it so it’s “kid friendly” at any age 😛

  2. I made these with different toppings — some with pepperoni & some with sauteed mushrooms. My super picky-eater teenager liked the pepperoni ones & said I should make them again (believe me, she hardly ever says that) – and my husband agreed (& appreciated that I made him some mushroom ones). Easy to make whatever people want for toppings! The dough was super sticky (used Stoneyfield lowfat Greek — so maybe that was the issue since not their O%). I added about 1/2 cup more flour and although it was still sticky, it baked up fine.

  3. Great, I weighed them and got only 13 for some reason but no matter they were great. Made part with peperoni and the other with mushrooms and some extra Penzey seasoning called “frozen pizza seasoning” which I find is good on lots of things and sauces etc. Very good, would make again.

  4. Found this through My Bizzy Kitchen’s FB post on Super Bowl apps. Going home to make these now for light dinner & I’ll freeze the rest. I already know they will be great since I’ve use the bagel dough to make pizza’s. I do want to thank you specifically for stating the brand & difference in the salt. It makes a huge difference when I don’t know which salt the recipe writer used & end up with an overly salted dish.

  5. I’ve made a lot of recipes from your blog over the years but this is one of the best. I did use bread flour because I was out of any other kind but it worked very well. My husband and I both loved these and thought these tasted WAY better than any premade pizza bites you could get at a store. I’ll definitely be making these again soon!

  6. Love doubling the recipe and keeping them on hand for the kids for a quick pre-practice snack or weekend lunch. I add chopped spinach for a little extra nutrition.

  7. Avatar photo
    Linda Parsons

    I’ve been wanting to try this dough for awhile now, and I am so glad I finally got to it! Absolutely love this recipe! Next I’m trying the bagels! 😋

  8. Made these today. My dough was really sticky and hard to form. I think I made a mistake somewhere along the way. Once baked though, the dough was crispy and these were delicious

    1. Amanda – different yogurts can make it really sticky, I’ve had to try different brands. Stonyfield works great! 

  9. Wow!  These are so good!  I can’t wait for my kids to get home from school to try them.  I think this is going to be a new alternative to frozen pizza we have so often on Fridays.  You’re recipes are SO good!

  10. Can i freeze these and would it be better to freeze them when assembled but uncooked or cook them and then freeze them ? 

    I want to make them ahead of time for a big party x

  11. These were so good! Made them for my 4 kiddos for Friday night pizza and movie night and they absolutely loved them! Thanks for a great recipe!

    1. Avatar photo
      Angelina Kishore

      Do you mean unbleached flour and whole wheat or unbleached or whole-wheat? 

      I have while whole wheat flour can I use 1 cup of that? 

  12. I haven’t made this yet, but I sent it to my sister as a potential packed lunch idea for my niece and nephew. She sent me a video of my niece, a very petite almost 2 year old, asking for more after her 3rd. They made them today with the plan to have the leftovers in their lunches the next day, only for there to be none leftover to pack!