These homemade bagel bites are chewy little snacks packed with flavor! Topped with cheese and your favorite toppings, they’re perfect for any time of day.
Making them is a fun project! I love getting creative with toppings. Sometimes I even sneak in some extra cheese—yummy! Just bake them until they’re golden, and enjoy!
Key Ingredients & Substitutions
All-Purpose Flour: This is the base of the dough, giving it structure. If you’re looking for a gluten-free option, you can try using a gluten-free all-purpose blend. However, the texture might be a little different.
Greek Yogurt: It keeps the bagel bites moist. If you’re dairy-free, plain almond or coconut yogurt works well as a substitute. I personally enjoy using Greek yogurt for its tangy flavor.
Cheese: Mozzarella and Parmesan bring cheesy goodness. You can try cheddar or any cheese you like! Just keep in mind that flavor will change slightly. For a vegan option, use plant-based cheese.
Pepperoni: Mini pepperoni gives a lovely punch. If you’re vegetarian, try toppings like olives, bell peppers, or mushrooms instead.
Italian Seasoning: This adds great flavor. You can also mix your own with dried basil, oregano, and thyme if you have them in your pantry.
What’s the Best Way to Shape These Bagel Bites?
Shaping your bagel bites properly helps them cook evenly and keeps that classic bagel look. Here’s how to do it:
- After kneading your dough, divide it into equal pieces to maintain uniformity.
- Roll each piece into a ball, then gently press it into the muffin tin.
- Use your thumb or finger to create a hole in the center, making sure to keep the sides thick enough to hold the toppings.
- Don’t worry if they look a bit rough; they’ll bake up beautifully!
For a nice finish, brush the tops with olive oil for that extra shine and crunch. Enjoy your cooking adventure!

Homemade Bagel Bites
Ingredients:
- 1 cup all-purpose flour
- 1 teaspoon baking powder
- 1/2 teaspoon salt
- 1 teaspoon sugar
- 2/3 cup plain Greek yogurt (or regular yogurt)
- 1/2 cup shredded mozzarella cheese
- 1/4 cup grated Parmesan cheese
- 20 small mini pepperoni slices or 10 regular pepperoni slices cut in half
- 1 tablespoon olive oil (optional, for brushing)
- 1 teaspoon Italian seasoning or everything bagel seasoning
- 1/4 cup shredded mozzarella or shredded cheese of choice for topping
- Marinara sauce (optional, for serving)
How Much Time Will You Need?
This recipe will take about 20 minutes of preparation and around 15-18 minutes to bake, making the total time about 35-40 minutes. You’ll have warm, gooey bagel bites ready to enjoy in no time!
Step-by-Step Instructions:
1. Preheat Your Oven:
Start by preheating your oven to 375°F (190°C). This will ensure your bagel bites bake evenly. Lightly grease a mini muffin tin or use silicone liners for easy removal later.
2. Mix Dry Ingredients:
In a medium-sized bowl, mix together the all-purpose flour, baking powder, salt, and sugar. This will set the base for your dough.
3. Add Yogurt:
Next, add the Greek yogurt to your dry mixture. Stir with a spoon or spatula until a soft dough forms. It may be slightly sticky—this is okay!
4. Knead the Dough:
Turn the dough out onto a floured surface. Knead it gently for a few minutes until it’s smoother. Don’t over-knead; you want a tender texture!
5. Shape the Dough:
Divide the dough into 12 equal pieces. Roll each piece into a ball. Press each ball into the muffin tin cups, and use your thumb to create a small hole in the center to give the bagel shape.
6. Add Cheese and Toppings:
Sprinkle a bit of shredded mozzarella and grated Parmesan at the bottom and sides of each bagel well. Next, add 2-3 slices of mini pepperoni on top and finish with a sprinkle of Italian or everything bagel seasoning.
7. Bake the Bagel Bites:
If you like a shiny finish, brush the edges lightly with olive oil. Now, pop them in the preheated oven and bake for 15-18 minutes or until they’re golden brown and the cheese is bubbling.
8. Cool and Serve:
Once baked, let them cool for a few minutes before carefully removing them from the muffin tin. Serve warm with marinara sauce on the side for dipping if you’d like. Enjoy your delicious homemade bagel bites!
These little snacks are perfect for parties, game days, or just a fun afternoon treat. Enjoy every cheesy, flavorful bite!
Can I Use Whole Wheat Flour Instead of All-Purpose Flour?
Absolutely! You can substitute whole wheat flour, but the texture may be slightly denser. Consider adding a little extra yogurt or water to keep the dough moist.
How Do I Store Leftover Bagel Bites?
Store them in an airtight container in the fridge for up to 3 days. To reheat, pop them in the microwave for about 20-30 seconds or place them in a preheated oven at 350°F (175°C) for about 5-7 minutes for a crispy texture.
Can I Freeze Bagel Bites?
Yes, you can freeze them! Prepare the bagel bites, bake them, and let them cool completely. Then, place them in a freezer-safe container or bag. They should last for up to 2 months. Reheat directly from the freezer, adding a few extra minutes to the baking time.
What Are Some Alternative Toppings?
Feel free to get creative! You can use diced vegetables like bell peppers or mushrooms, different cheeses, or even cooked bacon or crumbled sausage. The possibilities are endless!
