Homemade bagel bites with cheese and diced pepperoni

bagel bites cooking instructions

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I still remember racing home after school, throwing my backpack on the floor, and making a beeline for the freezer. Those tiny frozen Bagel Bites were the highlight of many afternoons, and honestly, I never quite outgrew my love for them. But as my cooking skills improved over the years, I started wondering—could I recreate that magic from scratch and maybe even make them better?

After countless test batches (and more than a few burnt tongues), I’ve finally nailed a homemade version that captures everything great about the original but with actual, you know, flavor. If you’re a hardcore fan like me, you’re going to love these chewy, cheesy, perfectly crispy little bites of nostalgia.

In This Recipe

There are two main parts to mastering homemade Bagel Bites:

  • Making mini bagels that don’t turn into hockey pucks
  • Nailing the topping and baking process

Why This Actually Works

Look, I’ve tried making these a bunch of different ways, and these techniques genuinely make a difference:

First off, baking the mini bagels on a wire rack is kind of a game-changer. It keeps the bottoms from getting too brown and hard, so they stay tender the way you want them.

Giving the split bagels a quick toast before adding toppings? That’s not me being fussy—it creates a barrier that stops the sauce from turning everything into a soggy mess. Trust me on this one.

And I know it seems like extra work to dice the pepperoni instead of using slices, but it distributes way better and actually tastes more like the original Bagel Bites we all grew up with.

Mini Bagels That Stay Tender

Here’s the thing about mini bagels—they’re cute as hell but they tend to get stale faster than regular-sized ones. It’s just math—more surface area relative to volume means they dry out quicker.

I found that weighing out 25-gram portions of dough gives you the perfect mini bagel size. But the real trick is in the baking setup. By placing the bagels on a parchment-lined wire rack set over a sheet pan, you slow down how fast heat hits the bottom of the bagels.

What you end up with is pretty magical—crisp on top but with a soft, chewy bottom. Just remember, once they’re baked, you’ve got about a 48-hour window to turn them into Bagel Bites before they start losing their mojo. Plan accordingly!

Topping and Baking

This is where the magic happens. Start by splitting those mini bagels and giving them a quick toast in a 350°F oven—just 5 minutes. Like I mentioned earlier, this step is crucial for preventing soggy bagels.

For the sauce, you want something with punch but not so much that it overwhelms everything else. Daniel’s Italian-American red sauce is perfect—simple but intense. Spread just a thin layer across each bagel half.

When it comes to cheese, I’ve tried them all, and finely shredded mozzarella is simply the way to go. Skip the pre-shredded stuff with all those anti-caking agents—take the extra minute to shred your own. It melts better, creates those awesome crispy edges, and the difference is obvious from the first bite.

Dice the pepperoni into small pieces instead of using whole slices. Yes, it’s an extra step, but it means every bite gets a perfect amount of pepperoni flavor, and it cooks more evenly too.

Once they’re assembled, bake at 425°F for about 8-10 minutes. You’re watching for that perfect moment when the cheese is fully melted and just starting to brown at the edges. When you nail the timing, you get this perfect harmony of textures—crispy, cheesy, saucy, and chewy all at once.

Recipe Details

bagel bites cooking instructions Makes 32 bits of awesomeness

  • Prep Time: 45 minutes
  • Cook Time: 25 minutes
  • Active Time: 1 hour
  • Chilling Time: 24 hours (mostly waiting)
  • Total Time: 26 hours (but worth every minute)

Ingredients

For the Bagels:

  • 500g bread flour
  • 10g kosher salt
  • 5g instant yeast
  • 300g cool water
  • 15g barley malt syrup (optional, but gives that real bagel flavor)

For the Toppings:

  • 1 cup Quick and Easy Italian-American Red Sauce
  • 1 teaspoon dried oregano
  • 1/2 teaspoon garlic powder
  • 1/4 teaspoon crushed red pepper flakes
  • 1/8 teaspoon ground fennel seed
  • 8 ounces low-moisture mozzarella cheese, finely shredded
  • 4 ounces pepperoni, finely diced

Directions

For the Mini Bagels:

  1. Throw the flour, salt, and yeast in your food processor and pulse a few times to mix.
  2. With the processor running, slowly pour in the water and barley malt syrup (if using) until a rough dough forms—about 30 seconds.
  3. Let the dough chill for 10 minutes, then process again for 45 seconds until it’s smooth and elastic.
  4. Dump the dough onto a lightly floured counter and divide into 32 equal pieces (about 25g each if you’re weighing).
  5. Roll each piece into a tight ball, then poke your thumb through the center to make a bagel shape with about a 1/2-inch hole.
  6. Line them up on a parchment-covered baking sheet, cover with plastic wrap, and refrigerate overnight (24 hours).

To Boil and Bake:

  1. Set your oven rack in the middle and preheat to 425°F.
  2. Get a 3-quart pot of water boiling. Meanwhile, set a wire rack over a half-sheet pan and line it with parchment.
  3. Boil the bagels in batches (4-6 at a time) for 30 seconds per side, then transfer them to your wire rack setup.
  4. Bake until they’re golden on top but still pale on the bottom, about 12-15 minutes.
  5. Let them cool completely—about half an hour. (You can store them in an airtight container for up to 48 hours before moving on.)

To Finish:

  1. Heat the oven to 350°F.
  2. Split the bagels horizontally and arrange them cut-side up.
  3. Toast them lightly for about 5 minutes.
  4. Crank the heat up to 425°F.
  5. Spread about a teaspoon of sauce on each bagel half.
  6. Sprinkle with your shredded cheese and diced pepperoni.
  7. Bake until the cheese is melted and just starting to brown at the edges, 8-10 minutes.
  8. Let them cool slightly so you don’t burn your mouth (learned that the hard way).

Special Equipment

  • 3-quart stainless steel pot
  • Food processor
  • Wire rack
  • Kitchen scale
  • Half sheet pan

Make Ahead and Storage

You can make the mini bagels up to 48 hours ahead and keep them in an airtight container at room temp. The sauce can be made a week ahead and kept in the fridge. Once you’ve assembled and baked them, they’re best eaten right away (duh), but you can refrigerate leftovers for up to 3 days and reheat them in a 350°F oven.

Nutrition Facts

Per Serving (2 Bagel Bites):

  • Calories: 180
  • Fat: 7g
  • Saturated Fat: 3g
  • Carbohydrates: 22g
  • Fiber: 1g
  • Protein: 8g
  • Sodium: 420mg

Look, I know making Bagel Bites from scratch sounds like a lot when you could just grab a box from the freezer. But the first time you bite into one of these—when you taste the difference between a real, freshly baked mini bagel and the freezer-burned pucks we grew up with—you’ll get it. They’re everything you remember, only better. Way better.

Whether you’re looking to relive some childhood memories or just want to make something fun and delicious, give these a shot. Your inner 12-year-old will thank you.

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