an overhead shot of 8 pizza bagels surrounded by basil, parmesan, and tomato sauce

pepperoni pizza bagels from scratch

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I love Bagel Bites as much as the next person, but if you’re ready to get serious about pizza bagels then you need to try making homemade pepperoni pizza bagels from scratch.

(Because when you know how to make pizza bagels from scratch, you can have pizza bagels anytime.)

Honestly, I’m a little bit obsessed with how well these pizza bagels turned out. I love homemade pizza and I love homemade bagels, so like, of course I had to combine them??? It was destiny or something. What does one do when they’ve achieved their life’s purpose? Because I kind of think I have.

Why this recipe works

These chewy pepperoni pizza bagels have a tomato basil bagel dough and are topped with whole pepperoni slices and a layer of mozzarella cheese. Literally a layer of mozzarella — instead of shredded mozzarella these pizza bagels are topped with bagel-shaped sliced of mozzarella, the kind you usually get at the deli for sandwiches.

an overhead shot of 8 pizza bagels surrounded by basil, parmesan, and tomato sauce

I laughed for a good 10 minutes alone in my kitchen when I saw my sheet pan of pizza bagels wearing what appeared to be wide-brimmed mozzarella sun hats ready for the oven. This is just a fun recipe, okay?

Pizza bagels are fun to make from scratch and they’re even more fun to eat. I hope you like them as much as I do!

Oh, and when I say this is a tomato basil pizza bagel dough I really, really mean it. There’s NO WATER in this dough. You’re getting MAXIMUM tomato flavor because the only liquid in the dough is tomato sauce. And the fresh basil combined with dried oregano and garlic powder just really adds that classic pizza flavor.

pizza bagel ingredient notes

What do you need to make pizza bagels from scratch? A lot of the same things regular bagels are made from with the addition of a few pizza-themed ingredients.

The biggest difference: There’s NO water in this tomato basil bagel dough! All of the liquid in this recipe comes from tomato sauce.

Tomato basil pizza bagel dough:

  • Bread flour – Bread flour has a higher protein content than all purpose flour and will give you a chewy, tender bagel. All purpose flour will “work” but your bagels will be denser, heavier, and dry out more quickly.
  • Salt-free tomato sauce – At room temperature or slightly warm. If you only have tomato sauce with salt, reduce the amount of salt in the recipe by ½ tsp. You can also use the reserved juices/liquid from a can of whole tomatoes or use warm tomato juice instead.
  • Yeast – I use instant yeast in all my recipes. If you only have active dry yeast, use 9 grams (1 TBSP) instead.
  • Salt – I use Diamond Crystal Kosher Salt which has a larger salt crystal. If you’re using another brand of salt, use half as much as the recipe calls for. If you’re measuring by weight, no need to adjust anything.
  • Sugar – Regular granulated sugar.
  • Garlic powder and dried oregano – Classic pizza flavors!
  • Fresh basil – Very thinly sliced (check out my post on how to chiffonade basil) so that it gets mixed into the dough evenly and you don’t have big basil chunks in your bagels.

Pepperoni pizza bagel toppings:

  • Pepperoni – Whatever brand your grocery store has. You’ll need 3-4 standard size pepperonis on each bagel. Avoid pepperoni “cups” because they’ll slide or fall off the bagels in the oven.
  • Thinly sliced mozzarella cheese – You can get it at your local deli counter or get one of the pre-sliced packages in the dairy aisle! Shredded mozzarella can work, but it tends to slide down into the middle of the bagel in the oven. The slices will give you an even mozzarella topping.
  • Parmesan cheese – I like to grate my own but you can totally use the pre-grated stuff too. You don’t need much of it! Just a light dusting before or after the oven. (Or both!)

what to put on pizza bagels

When you’ve got a tomato basil bagel with this much flavor AND whole pepperonis and cheese on top, how the heck do you even eat it? Honestly, exactly the same way you’d eat a plain bagel. I usually toast mine with cream cheese or soft goat cheese, which works ridiculously well, but there are so many other great options too.

  • Cream cheese – Sprinkle with Pepperoni Minis as a nice treat.
  • Tomato or pizza sauce with shredded mozzarella and pepperoni – Double pizza bagels! Bake open-faced for 15 minutes at 350F. If you’re going this route, you may want to skip the mozzarella and pepperoni on top of the bagels but you do you!
  • Veggie cream cheese – The veggie flavors are right at home with the tomato basil bagel flavors.
  • Caprese sandwich – Thick tomato slices or a sun-dried tomato pesto, fresh basil, and slices of fresh mozzarella.
  • Caramelized onions and soft goat cheese – The sweet onions and tangy goat cheese work so well with these.
an overhead shot of pizza bagels. one has been sliced in half with cream cheese and mini pepperonis on it.

how to shape a bagel

Divide your dough. If combining a few smaller pieces, stack them with the smallest on top.
Fold all the edges of the dough across the center creating a smooth surface against the counter.
Flip the dough smooth side up. In a cupped hand, slide it toward you. Rotate 90 degrees and repeat.
Flip the dough over and use flour-coated hands to poke a thumb through the “seam” at the bottom.
Stick your other thumb in and squeeze while rotating the dough to stretch it.
Stretch, don’t tear. The hole will shrink when it bakes. It should be ~1/3 the width of the bagel.
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how to store pizza bagels

Pizza bagels are best eaten within a day or two of making. If you’re planning on storing your bagels for longer than that, slice and freeze.

For food safety reasons, you don’t want to leave the cheese and pepperoni out at room temperature for too long.

You can read more about the best ways to store bagels in my post: Do bagels need to be refrigerated?

a pile of four pizza bagels and a bunch of fresh basil

a few quick recipe notes

  • I used these round cutters to cut my mozzarella slices into a bagel shape. I used the biggest ring and the second-smallest ring. You don’t have to cut the slices to fit perfectly, but I found it helped prevent the mozzarella from getting pulled into the bagel hole when it melted.
  • Line your sheet pan with a silicone mat or parchment paper for easy cheese cleanup. Greasing your sheet pan isn’t enough — the cheese is also greasy and the bagels have a gelatinized exterior from the boiling. They will stick to the pan.
  • If you decide to use shredded mozzarella use finely shredded mozzarella and don’t skip the egg wash. The egg was helps the cheese stick to the sides of the bagel, so it doesn’t slide off the sides or into the bagel hole.
  • This dough takes longer to come together than plain bagel dough. Be patient with it. Because there’s no water in the dough, it takes the flour a little longer to absorb the tomato sauce. If there’s still a lot of dry floury bits in the bowl after 5 minutes, scrape down the bowl and add 1 tsp warm water, sprinkling it onto the dry flour and letting the mixer run for at least 30 seconds before deciding if you need to add more. There’s more water in the tomato sauce than you think — the flour will fully absorb it while it kneads and rests, so really avoid adding more water unless you absolutely need to.
  • Many thanks to Erin for helping me brainstorm tomato based products to try in recipe testing!

pizza bagels FAQ

Can I make these pizza bagels in my air fryer?

I haven’t tested this but I think you can! An air fryer is a convection oven so reduce the temp by 25 degrees and reduce the baking time to 15 minutes. When a thermometer inserted into a bagel reads between 190-210F, they’re done.

Can I reheat pizza bagels in the microwave?

Yep! The cheese might start to separate a little bit from the dough, but you definitely can.

What do you eat as a side dish with pizza bagels?

Anything you usually eat with pizza goes great with pizza bagels. Caesar salad, giant stuffed arancini, chopped caprese and avocado salad, iceberg salad with ranch dressing, one-skillet cacio e pepe rigatoni, garlic fries, mozzarella sticks, veggie sticks with spinach and artichoke dip, garlic bread, Greek salad…

Is there anything else can I use instead of tomato sauce?

V8 juice, tomato juice, or whatever juices are left in a can of whole peeled tomatoes. I tested this recipe with crushed tomatoes and fire roasted tomatoes and was very disappointed in how little flavor they added.

Do I need to use bread flour?

Even though I’m on record saying it’s okay to use all purpose flour in my plain bagel recipe, the reason to use bread flour for pepperoni pizza bagels is because there’s no water in this dough. The tomato basil bagel dough needs as much extra help it can get to develop gluten and give you a nice rise and chewy texture. Bread flour will do that much better than all purpose flour.

Why are your volume measurements for the flour and tomato sauce “approximate”?

I’ve given the cup measurements as an approximate in case it’s helpful for you, but you’ll get the best results measuring the tomato sauce and flour with a scale. The ratio of flour to tomato sauce is super important for getting the dough to the right texture. A kitchen scale is worth it, I promise.

FWIW — I don’t test my recipes with volume measurements. I test them using a kitchen scale to weigh the ingredients. I used an online ingredient converter to figure out how many cups of flour and tomato sauce that would be but I can’t guarantee how accurate it is.

Depending on how you scoop your flour you might end up with more or less than I did! And depending on what brand of measuring cups you use, you might end up with more or less tomato sauce than I used.

If you decide to use cup measurements just know you might need to add more flour (if the dough is too wet) or more tomato sauce (if the dough is dry) to get the dough to the right consistency!

I’m vegetarian. Do I need to use pepperoni?

No you do not!

a pizza bagel sliced in half with cream cheese on it. the top half is slightly offset. more pizza bagels are behind it.

pizza bagels from scratch

These aren't your freezer section's pizza bagels! These homemade pizza bagels bring that classic pizza flavor thanks to a tomato basil bagel dough and a pepperoni and mozzarella cheese topping.
5 from 1 vote
Prep Time 15 mins
Cook Time 20 mins
Resting time 1 hr 30 mins
Total Time 2 hrs 5 mins
Course Breakfast
Cuisine American, Italian
Servings 8 bagels


  • 500 grams bread flour (approximately 3½ cups)
  • 356 grams salt-free tomato sauce (approximately 1½ cups, at room temperature)
  • 18 grams sugar (1½ TBSP)
  • 6 grams instant yeast (2 tsp)
  • 5 grams diamond crystal kosher salt (1½ tsp, use ¾ tsp of another brand, no need to adjust if weighing)
  • 1 tsp dried oregano
  • ½ tsp garlic powder
  • 6-7 basil leaves (thinly sliced)
  • ½ TBSP warm water (only if needed)
  • 1 egg (for egg wash)
  • 8 slices low-moisture mozzarella cheese
  • 24 pepperoni slices
  • parmesan cheese (finely grated, for topping)


  • Combine flour, salt, sugar, and yeast in the bowl of a stand mixer, making sure the salt and yeast aren't touching. Pour the tomato sauce into the center of the bowl along with the oregano and garlic powder. Mix on low speed until the dough comes together on the dough hook, pausing occasionally to push dry ingredients into the center.
  • If there are still quite a lot of dry ingredients in the bottom of the bowl after about 5 minutes, add up to 1½ TBSP warm water 1 teaspoon at a time, sprinkling it onto the dry spots in the bowl and letting the mixer run for at least 30-60 seconds before deciding if you need to add more water.
    Resist adding water unless absolutely necessary. The dough will hydrate more fully as it rests. It's better to have a slightly dry bagel dough than a dough that's too wet.
  • Add the thinly sliced fresh basil and increase speed to medium. Knead 3 minutes until dough is smooth, tacky, and slightly stretchy.
  • Tuck the ends under the dough to shape it into a ball, then place in a lightly oiled bowl, cover, and let rise for 1 hour in a warm spot. It should just about double in size and when you press a finger into it, the indentation should spring back slightly.
  • Gently deflate the dough, knocking the air bubbles out of it. Cover and let rest 10 minutes.
  • Preheat your oven to 425°F and bring a wide, deep pan or large pot filled with at least 3 inches of water to a low boil on the stove.
  • Divide the dough into 8 equal pieces with a kitchen scale. Shape them into balls by gently flattening each piece against a clean, un-floured countertop, folding the edges into the center and pinching them together to form a smooth surface on the underside of the dough.
    Flip the dough over so the smooth side is on top. Cup your hand around the dough ball in a claw shape with your pinkie against the counter, and drag your hand towards your body. Rotate the dough 90 degrees and repeat as needed until you have a smooth ball with a seam on the bottom.
  • Dust your hands with in flour and poke a thumb through the seam-side of each dough ball, pushing any stray edges into the middle. Slide your other thumb in and gently rotate the bagel ring through your hands, stretching the dough until the hole in the middle is twice as wide as the sides of the bagel.
  • Arrange the bagels on a silicone or parchment lined sheet pan. Cover with a damp paper towel and let them rest for 10 minutes.
  • While the bagels rest, use a large (3") and a small (1") round cutter to cut 8 mozzarella slices into bagel shapes.
  • Immediately before boiling, stretch the bagels again so the holes are twice as wide as the sides. Then slide them into the pot of boiling water, top-side down. Work in batches of 2-4, depending on how big your pot is.
  • Boil bagels for 1 minute per side, then use a wire spider to return them to the baking sheet.
  • Brush bagels with egg wash, then top each pizza bagel with 4 pepperoni slices, a ring of thinly sliced mozzarella cheese, and a dusting of parmesan cheese.
  • Bake for 20 minutes at 425°F.
  • Remove the bagels from the oven and transfer immediately to a wire rack to cool completely.


  • To test if your dough is ready after it rests for an hour, gently press into it with one finger. If it immediately fills in the indentation when you remove your finger, your dough needs more time to rise. If the indentation only fills in part way or fills in very slowly, your dough is ready. If it doesn’t fill in at all or the dough seems to collapse, your dough has overproofed.
  • You can mix in a 1/4 cup of your preferred topping right into the dough to infuse your bagels with maximum flavor. Just make sure your topping doesn’t include salt, or it can throw off the chemistry of the dough.
  • Store in an airtight bag with a paper towel to absorb moisture. Stored properly, they will stay good for 3-4 days. They’ll get a bit hard after the first day or so, but soften up if you toast them. You can also run them briefly under water (!!!), then microwave them for 10 seconds, slice them, and toast them (or put them on a rack in your regular oven for 10 minutes at 350°F).
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5 stars
These were so good! Absolutely will make again, maybe with Jalapeno for a little kick! Thanks so much!