These Keto Pepperoni Pizza Bagels are chewy, cheesy, and way better than the freezer kind you grew up on. Made with low carb bagels, loaded with tasty toppings and baked until golden they’re everything you want in a quick pizza fix.

Jump to:

• ❤️ Why You'll Love This Pepperoni Pizza Bagels Recipe
• 🛒 Ingredients for Pizza Bagels
• 🔪 How to Make Keto Pizza Bagels
• ☑️ Storage Instructions
• 🍴 What to Serve with Pizza Bagels
• 💡 Tips
• 🔄 Substitutions and Additions
• Is Fathead Pizza Keto?
• Can I Make These Ahead of Time and Bake Later?
• Why Did My Bagels Soggy Underneath?
• How do I Make Them Crispier?
• What’s the Best Way to Reheat Leftovers?
• 🍽️ Even More Keto Pizza Recipes

❤️ Why You'll Love This Pepperoni Pizza Bagels Recipe

• Chewy and cheesy bagels
• Topped with pizza sauce, mozzarella cheese and pepperoni
• Baked to perfection
• Keto friendly alternative to the popular frozen version
• Gluten-free and kid friendly

These Keto Pepperoni Pizza Bagels skip the traditional crust and go straight for the good stuff. Each one starts with a chewy bagel half, layered with sauce, melty mozzarella, and crispy mini pepperoni. They bake up golden, bubbly and loaded with all those classic pizza flavors you love.

I’ve made them for lunch, party appetizers or just random snack attacks, and they always hit the spot. What I love the most is the are made with better ingredients and zero gluten than the frozen ones. No one ever asks if they’re Keto; they’re too busy going back for more.

And if you like this recipe, you’ll want to check out my Pizza Bowls or Crustless Pizza too. They’ve got all the same flavors, just in different forms. Great for days when you’re skipping the bagel but still want something cheesy and saucy.

🛒 Ingredients for Pizza Bagels

• Keto Fathead Bagels: Gives a sturdy, chewy base that holds up to sauce and toppings
• Mozzarella cheese: Melts evenly and gives that gooey, stretchy texture.
• Keto Pizza Sauce: Adds rich tomato flavor and classic pizza seasoning.
• Mini pepperoni: Adds salty, crispy bites with delicious pizza flavor.

*Exact measurements are listed in the recipe card below.

🥣 Recommended Tools

• Baking sheet
• Parchment paper

🔪 How to Make Keto Pizza Bagels

Prepare a batch of Keto Fathead Bagels according to the directions. Then allow them to cool before slicing them in half and placing them, cut side up, on a parchment paper lined baking sheet.

Spread the pizza sauce over the tops of each bagel half.

Top with shredded mozzarella cheese.

Add the mini pepperoni slices and bake for 7-10 minutes or until the cheese is melted and golden.

Allow the bagels to cool slightly before serving.

☑️ Storage Instructions

Fridge: Store leftovers in an airtight container for up to 3 days

Freezer: Freeze the pizzas on a baking sheet first, then transfer to a freezer-safe bag for up to 2 months

🍴 What to Serve with Pizza Bagels

• Air Fryer Zucchini: Tender, garlicky zucchini rounds that crisp up beautifully and cut through the richness.

• Air Fryer Broccoli: Caramelized broccoli florets with garlic‑olive oil and a hit of Romano.

• Sautéed Shredded Brussels Sprouts: Finely shredded and lightly pan‑fried, with a sprinkle of Parmesan for flavor balance.

• Cauliflower Mushroom Risotto: Creamy, low‑carb cauliflower rice dressed up like risotto to soak in extra sauce.

• Simple Green Salad: Think crisp romaine, cucumber, with homemade Italian Dressing or Caesar Dressing.

• Caprese Salad: juicy tomato, creamy mozzarella, basil, and balsamic drizzle for a bright contrast.

💡 Tips

• Let the bagels cool before slicing so they don’t squish under the knife.
• Use parchment paper on the baking sheet for easy cleanup and no sticking.
• Don’t overload with cheese or it can slide off the edges while baking.
• Mini pepperoni works best because it crisps up quickly and stays put.
• Bake until the cheese is just starting to brown for the best texture.
• For faster prep, you can pre-slice and refrigerate the bagels up to a day ahead.

🔄 Substitutions and Additions

Let's face it, there's no such thing as too much pizza! And there are so many ways to make it your own! If you're looking for some inspiration, here are some great ideas:

• Ground beef: Swap the pepperoni for ground beef. You'll want to add seasonings to the beef to give it a little extra flavor. I use this homemade dry Italian Dressing Mix in mine.

• Spinach: Add a few spinach leaves for a burst of freshness and added vitamins and minerals.

• Fresh tomatoes: Slice some vibrant cherry tomatoes and scatter them over the pizza bowl for a burst of tanginess.

• Cheese: You can use any of your favorite melting cheese like cheddar or provolone. Or for a tangy twist, try adding a little salty feta cheese or creamy goat cheese.

• Bacon: Everything is better with bacon! Cook up crispy bacon or pancetta and crumble it over the pizza bowl to elevate the smoky flavor.

• Red onion: Thinly sliced red onion makes a great addition. Because they cook quickly, you'll probably want to sauté onions before adding them.

• Red pepper flakes: For those who enjoy a bit of heat, add just a pinch of red pepper flakes to spice things up.

• Chicken: Do you have leftover chicken? Use it! Whether it's leftover roasted chicken or store-bought rotisserie, chicken adds lean protein and is a hearty addition.

• Fresh basil: Fragrant fresh basil leaves on top adds so much flavor and a pop of green color.

• Artichoke hearts: Add chopped, marinated artichoke hearts for little bites of tangy flavor.

• Mushrooms: These Marinated Mushrooms are amazing on pizza and double as a great source of protein.

• Alfredo: For a completely different take on Keto pizza, you can use this easy to make Alfredo Sauce with shredded chicken.

Is Fathead Pizza Keto?

It sure is! It is naturally gluten free and grain free. Made from all Keto friendly ingredients, like almond flour and mozzarella, this amazing recipe is a game changer for those on Keto or low carb diets!

Can I Make These Ahead of Time and Bake Later?

Yes. Assemble them, cover, and refrigerate. Bake when ready to serve.

Why Did My Bagels Soggy Underneath?

That can happen if they’re too warm when topped. Make sure they’re completely cooled before you add anything.

How do I Make Them Crispier?

You can bake a couple extra minutes or place them on the top oven rack to help the edges brown.

What’s the Best Way to Reheat Leftovers?

A toaster oven or air fryer works best to bring back the crisp edges without drying them out.

🍽️ Even More Keto Pizza Recipes

• Pizza Stuffed Peppers
• Portobello Mini Pizza
• Cauliflower Pizza Crust
• Pizza with Fathead Dough

*Originally published on May 27, 2018, updated on July 29, 2025 with improvements to the recipe, new photos, new recipe information and helpful tips.