August 23, 2021

Easy 30 Minute Homemade Pizza Bagels

Your favorite freezer meal as a kid but healthier. These easy 30 minute Homemade Pizza Bagels are made with whole grains, low-fat cheese, and turkey pepperoni but still have all the delicious comforting flavors you remember.

I don't know about you, but as a kid, my mom always had a giant stash of mini bagel bites in the freezer for an after school snack or quick Sunday lunch after church. My brothers and I could go through an entire package in one sitting if she wasn't paying attention!

Unlike Hot Pockets, where the outside was boiling lava hot and the inside was frozen (ikyk), these little bagel bites were crispy, cheesy, and just the best.

Then you grow up and society says you can have them in your house if you have kids... and you shouldn't eat them because they're not healthy... how fair is that?

So I decided to write a healthy pizza bagel recipe you can make at home anytime without the guilt. That's right - today's recipe is homemade pizza bagels! They're everything you love about frozen bagel bites but adult-sized and healthy!

And, if you're that mom that wants a healthier alternative for your kid's snacks, this one is for you. You can feel good about giving these pizza bagels to your kids!

Homemade pizza bagels on parchment paper

What are pizza bagels made of?

The frozen mini bagel bites are made with mini white bagels, sauce, full fat cheese, and baby pepperoni and sausage cubes. They're mostly bagel with a hint of saucey cheese (which is why kids love them so much haha) and that's really it.

THESE homemade pizza bagels are made with whole grain bagels, low-fat cheese, and full-size turkey pepperoni. The ratio of bread to cheese to pepperoni is PERFECT and they are so incredibly addicting!

All you'll need to make these easy pizza bagels is:

  • Skinny whole wheat bagels: these are the thin cousins of regular whole wheat bagels. I love this brand, but feel free to use any brand you like!
  • Pasta sauce: store-bought or homemade, whatever you like!
  • Low-fat shredded mozzarella: to keep the macros balanced. We're keeping the creamy cheese without too much saturated fat!
  • Turkey pepperoni: a healthier alternative to traditional pepperoni. I just use whatever brand is cheapest at the store, but you'll need exactly 80 slices.
  • Seasonings: a simple blend of italian seasoning, garlic powder, and red chili flakes to take these bagels to the next level!

Ingredients for homemade pizza bagels

How to make homemade pizza bagels - two ways!

Yes, you read that right, two ways! This healthy pizza bagel recipe can be made on a sheet pan in the oven or in batches in an air fryer. However you decide to make them, they'll turn out crispy, cheesy, and just like your childhood!

Pizza bagels in the oven

Set out all your ingredients and prepare the pizza bagels per recipe instructions. Spread aluminum foil over a baking sheet, then lay a cooling rack over the sheet pan.

Place 8 of the bagel bites on the rack and cook for 10-12 minutes, then cook the second batch.

Pizza bagels in the air fryer

Set out all your ingredients and prepare the pizza bagels per recipe instructions. Spray the tray of your air fryer with cooking spray, then place your homemade pizza bagels in a flat layer on the tray.

Bake for 5-8 minutes at 400°F until the cheese has melted and the bagels are crispy.

If you've been looking for an air fryer but aren't sure which one to get, you totally have to get this Instant Pot Air Fryer attachment.

Instead of buying a whole other appliance, all you need is this magical lid attachment that replaces the traditional Instant Pot lid. You use the same metal pot, but add in a frying basket and you're good to go! I absolutely love it.

A pizza bagel with a bite out of it

Why this healthy pizza bagel recipe works

  1. It's so easy: just a few simple ingredients and 30 minutes is all you need!
  2. It's better than the original: not even kidding! There's more flavor, more nutrient-dense ingredients, and a better ratio of bread to cheese to meat, not to mention these are much bigger!
  3. It's macro-friendly: unlike the original bagel bites, these homemade pizza bagels have a good ratio of carbs, fats, and proteins. For 3 mini bagel bites, it's 158cal / 4.5F / 23C / 0P; for 1 large homemade pizza bagel, it's 138cal / 5.5F / 10C / 10P. In layman's terms, the Ka Pai Cooking recipe has complex carbs, more fiber, and 10x the amount of protein compared to the original.
  4. It's kid-friendly: this healthy pizza bagel recipe was adapted from a classic kid's food, right? But you can actually feel good about what in these bagels!
  5. It's freezer-friendly: just like the original, you can pull these bagels out of the freezer and reheat them in the oven!
  6. It's customizable: I stuck with the traditional "pepperoni pizza" bagel, but you could always add sausage crumbles, olives, peppers and onions, or even do diced ham and pineapple! The combinations are totally up to you.

Frequently asked questions

Can these be made gluten-free?

Yes! Just know they'll be a little more calorie dense with more carbs per serving. I've had a hard time finding "skinny gluten-free whole wheat bagels" at my local grocery stores, so just use whatever gluten-free whole wheat bagels you can find.

Can these be made dairy-free?

Of course! Just use your favorite non-dairy mozzarella cheese substitute.

How long do pizza bagels last?

Once they've been cooked, store your pizza bagels in the fridge for up to 72 hours in an air-tight container. Simply reheat in the microwave until warm to serve.

Can I freeze homemade bagel bites?

Yes! If you want to make these ahead of time as a meal prep snack, let them cool completely at room temperature after baking, then wrap individually in foil and store in a ziploc bag for up to 3 months.

To reheat, warm in the oven until heated through and the cheese is melted again.

Homemade bagel bites with pepperoni and seasonings on top

Since we're on a pizza kick, be sure to try my Whole Wheat BBQ Chicken Pizza recipe too! The dough is ready in 10 minutes (no yeast required!) and the whole family will love it! You can also click here for more easy snack ideas.

Please leave a star rating and review below if you try this recipe so other readers know how you liked it! I also love hearing how much you and your families enjoy my recipes. Enjoy!

Your favorite freezer meal as a kid but healthier. These easy 30 minute Homemade Pizza Bagels are made with whole grains, low-fat cheese, and turkey pepperoni but still have all the delicious comforting flavors you remember.


Brooke Harmer













  • 8 ct. Bubba's Skinny Whole Wheat Bagels*
  • 1 C pizza sauce
  • 3 C low-fat shredded mozzarella cheese*
  • 5 oz. turkey pepperoni (about 80 slices)
  • Italian seasoning (optional)
  • Red chili flakes (optional)
  • Garlic salt (optional)


  1. Preheat the oven to 400°F and line a baking sheet** with foil, then place a cooling rack on top of the foil. Set aside.
  2. Slice each bagel in half along the perforated line so you end up with 16 total bagels. Spread 1 tablespoon pizza sauce around the bagel, then top with 3 tablespoons cheese and 5 turkey pepperoni. Repeat with each bagel until all the ingredients are finished. Sprinkle desired seasonings on top of bagels.
  3. Arrange 8 of the bagels on the prepared sheet pan and bake for 10-12 minutes. Repeat with the remaining bagels. Let sit for 5 minutes before serving.


*See blog post for gluten-free and dairy-free options.

**See blog post for using the air fryer instead of the oven.

Nutrition facts are a calculated estimate for one bagel.


Serving: 1 bagel / Calories: 138 / Fat: 5.5g / Saturated Fat: 3.1g / Sodium: 438mg / Carbohydrates: 12.3g / Fiber: 2.6g / Protein: 10.1g