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    Home » Breads » Bagels

    Cheesy Tomato Basil Pepperoni Bagels

    5 from 7 votes
    Published by Rebecca Eisenberg ⁠— July 19, 2021 (updated October 23, 2026) — 9 Comments

    979 shares
    Jump to Recipe Jump to Video

    This post may contain affiliate links

    homemade pepperoni pizza bagels

    I love frozen Bagel Bites as much as the next person, but if you're ready to get serious about pizza bagels, then you need to try these tomato basil pepperoni bagels. To give them the most amazing pizza sauce flavor, I replaced all the water in my usual bagel dough with tomato sauce. So these pizza bagels are made from a tomato-basil bagel dough, and then they are topped with whole pepperoni slices and a crispy layer of mozzarella cheese for the best pizza bagels you'll ever eat. I hope you like them as much as I do!

    Eight pizza bagels made from scratch arranged on parchment paper, surrounded by pepperoni slices, a wedge of cheese, fresh basil leaves, and a small bowl of dried herbs.

    Honestly, I'm a little bit obsessed with how well these tomato basil pepperoni bagels turned out. I love pizza and I love bagels, so of course I had to combine them.

    Oh, and when I say this is a tomato basil flavored bagel dough I really, really mean it. There's NO WATER in this dough. The only liquid in the dough is tomato sauce. The addition of fresh basil, dried oregano, and garlic powder just really emphasizes that classic pizza flavor.

    Unlike my other easy bagel recipes, which use all-purpose flour, I do use bread flour in this pizza bagel recipe. Because the only liquid in this dough comes from the tomato sauce, I found it made a huge difference when I used a high-protein flour that could provide a lot of structure and elasticity.

    A bit of very thinly sliced fresh basil really brings that pizza flavor alive, but you do want to make sure it is truly sliced very thin so that it gets mixed into the dough evenly (check out my post on how to chiffonade basil for tips on slicing basil).

    Instead of shredded mozzarella, I top my pizza bagels with bagel-shaped slices of mozzarella, the kind you usually get at the deli for sandwiches. When I tested different ways of putting cheese on top of my pizza bagels, I found that while shredded mozzarella can work, it tended to slide down into the middle of the bagel in the oven. Using the sliced mozzarella gave a nice, even, crispy mozzarella topping.

    I used these round cutters to cut my mozzarella slices into a bagel shape. 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.

    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?

    A stack of pepperoni pizza bagels from scratch on parchment paper, with one bagel halved and spread with cream cheese.
    A pizza bagel made from scratch, sliced and topped with melted cheese, with one half spread with cream cheese, accompanied by pepperoni, a garlic bulb, and fresh basil leaves on parchment paper.

    Be patient with this bagel dough

    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 teaspoon 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.

    Roll-And-Poke Bagel Shaping Method

    Divide the dough into equal portions on an unfloured surface. If you're combining a few pieces together to make a portion, stack the smaller pieces on top of the bigger pieces. Tuck the edges up so the dough is smooth against the counter with a seam pinched together on top. Repeat until the dough ball feels fairly tight. Don't tear the dough, just stretch it.

    Then, flip the dough over so the seam side is down against the counter. Cup your hand around the dough and slide it toward you. The dough will take on an oval shape. Rotate it 90 degrees and repeat to turn the oval into a round circle.

    (Or, cup your hand around the dough with your pinkie-side flush against an unfloured counter and your thumb and forefinger making an O- or C-like shape above the dough. Move your hand in quick circles without picking your pinkie off the counter, and the dough will quickly shape itself into a nice smooth ball of dough.)

    animated gif: pieces of dough stacked on top of each other with the smaller pieces on top of the bigger ones
    step 1: stack dough
    animated gif: the edges of the bagel dough being tucked up hiding the smaller pieces in the center
    step 2: tuck the edges up
    animated gif: a hand cupped around a ball of dough. the dough is dragged forward, the surface tension shaping it into a smooth ball.
    step 3: flip and slide
    [gif] a thumb pokes a hole through the bottom of a round ball of dough
    step 4: poke a hole
    [gif] two thumbs through the hole in the bagel dough rotating it and gentle stretching it
    step 5: stretch
    [gif] a fully stretched out round of bagel dough
    step 6: stretch some more

    Once the dough has been shaped into balls, coat your hands in flour and stick a thumb through the bottom seam of the dough. Slide your other thumb in and gently squeeze and stretch, rotating the dough through your hands until the bagel hole is at least the same width as the sides of the bagel if not bigger.

    You may want to repeat the stretching process again before boiling to keep the hole from closing up in the oven.

    What I Put on Cheesy Pepperoni 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.
    • Use them to make pizza bagels - Double pizza bagels! Bake open-faced for 15 minutes at 350°F. 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 homemade goat cheese work so well with these.
    A pile of pizza bagels from scratch topped with melted cheese, with one bagel cut in half and spread with cream cheese and pepperoni slices, surrounded by garlic, basil, and pepperoni.
    A stack of four homemade pizza bagels topped with cheese, set next to a bunch of fresh basil and a small wooden spoon of spices.

    💭 Have More Bagel Questions?

    I've rounded up answers to common bagel questions and how-to guides, including:

    • How to knead bagel dough by hand and what it should feel like
    • Why bagels are always boiled
    • Step-by-step guides for bagel shaping and baking techniques

    See my bagel-making 101 guide for more! 

    📖 Recipe

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

    Tomato Basil Pepperoni Bagels

    Servings 8 bagels
    Author Rebecca Eisenberg
    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.
    Print Recipe Email Recipe Pin Recipe
    Prep Time 15 minutes mins
    Cook Time 20 minutes mins
    Resting time 1 hour hr 30 minutes mins
    Total Time 2 hours hrs 5 minutes mins

    Recipe Notes

    • Store in an airtight bag with a paper towel to absorb moisture. 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. 
    • Line your sheet pan with 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 wash helps the cheese stick to the sides of the bagel, so it doesn't slide off the sides or into the bagel hole.

    Ingredients
     

    • 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 teaspoon of another brand, no need to adjust if weighing)
    • 1 teaspoon dried oregano
    • ½ teaspoon garlic powder
    • 6-7 basil leaves (thinly sliced)
    • ½ tablespoon 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)

    Instructions
     
    Prevent your screen from going dark

    • 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 tablespoon 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 in a warm spot until it just about doubles in size, about 1 hour.
    • Use the fingerprint test to check if the dough is ready.
    • 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.
    Liked it? Rate this Recipe!

    Video

    BagelsBasilTomato
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    Comments

      5 from 7 votes (1 rating without comment)

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      Recipe Rating




    1. Samantha says

      July 28, 2021 at 9:29 am

      5 stars
      These were so good! Absolutely will make again, maybe with Jalapeno for a little kick! Thanks so much!

      Reply
      • Rebecca says

        July 28, 2021 at 9:44 am

        omg jalapeno sounds like a great addition! glad you liked them 🙂

        Reply
      • Bekah says

        September 30, 2022 at 6:44 pm

        5 stars
        These were soooo tasty! Basically pizza bagels. 😋 It was also my first time making bagels and Rebecca’s steps for shaping were super helpful.

        Reply
    2. Amy says

      March 26, 2022 at 9:37 pm

      5 stars
      This recipe was perfect for pizza burgers and delicious with artichoke hearts. Definitely family friendly and pretty easy to make.

      Since I was out of sliced mozzarella, I used sliced Munster and co-jack, which worked way better than the shredded mozzarella I tried with a few.

      Reply
      • nicole says

        January 23, 2023 at 7:43 pm

        5 stars
        omg burger buns, genius! thank you kind stranger for blowing my mind, i will be absolutely making pizza burgers with these :O

        Reply
    3. nicole says

      January 23, 2023 at 7:41 pm

      5 stars
      i was scared of bagels for ages and im so glad i finally made these, because oh my gosh, they were *easy*! and delicious! i did not expect that at all XD think of all the years ive wasted not making my own bagels. im going to be an unstoppable bagel making machine now, seeing other comments about adding jalepeno and using these as BURGER BUNS?! ohhhh yes, we will be doing those things.

      seriously though, these were so approachable and come together quickly with the stand mixer. i think we didnt knead enough, so our dough was a little less silky smooth than the one we saw on the instagram video and therefore a little more uneven/ugly when made into bagel shape, but thats an easy fix for next time. and honestly, they tasted A+ so im not concerned. we also used pepperoni we cut from a stick and unfortunately they went rouge and cupped XD so if we use the same again i will probably cut notches in the rounds to discourage that, or buy the presliced deli stuff. again it was only an aesthetic thing, they still tasted fab. im really exited to make these again! and setting my sights on those cheddar jalapeno ones next 😀

      Reply
    4. Brittany Ogden says

      November 12, 2023 at 7:58 pm

      Would this be fairly easy to convert to gluten free?

      Reply
      • Rebecca Eisenberg says

        November 13, 2023 at 1:25 pm

        I'm not sure though people have said that they've had some success using some of the cup-for-cup flours in my bagel recipes. I haven't personally tried it. If you do, let me know how it goes!

        Reply
    5. Heather says

      April 22, 2026 at 8:28 am

      5 stars
      Growing up a latch key kid, & raised on Bagel Bites, I had to try this recipe.
      Rebecca has taught me everything I know about making bread, and I couldn't be happier with this recipe. Her videos made understanding the steps easy (I only learned to cook 3 years ago), and the whole house smelled Amazing from the basil. I out in my pre-order for the book. 😊

      Reply
    rebecca wearing a black t-shirt with her left hand on her hip and her right hand holding a whisk upright

    Hi, I'm Rebecca! I'm a pastry chef with a home cook mentality and New York Times bestselling author of Small-Batch Breads. I'm on a mission to make spending time in the kitchen fun and accessible — that's why so many people love my beginner-friendly bread recipes. I'm always looking for new and creative ways to get the most out of my favorite ingredients and flavors!

    More about me →

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    Journalist turned pastry chef, on a mission to make cooking and baking fun and accessible. I'm always looking for new and creative ways to get the most out of my favorite ingredients and flavors! A Pittsburgh native currently calling Boston home.

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