If you have ever wished for a snack that combines irresistible flavor, convenience, and a solid protein boost, your wish just came true with this High-Protein Bagel Bites Recipe. These bites are a perfect marriage of soft, tangy dough wrapped around rich, melty cream cheese, all topped with classic bagel seasonings that make every bite pop with flavor. Whether you need a quick breakfast fix, a midday pick-me-up, or an impressive appetizer, this recipe will quickly become your go-to for satisfying hunger while keeping things wholesome.

Ingredients You’ll Need
Getting this High-Protein Bagel Bites Recipe just right means using a handful of simple, high-quality ingredients. Each one plays a vital role in building those perfect textures and flavors that make these bites truly addictive.
- 1 cup all-purpose flour (or whole wheat flour): The base that provides structure and a tender crumb to the dough.
- 2 tsp baking powder: Helps the dough rise and become fluffy on the inside.
- ½ tsp salt: Balances the flavors and enhances the dough’s overall taste.
- 1 cup plain Greek yogurt: Adds moisture, tang, and a fantastic protein punch.
- 1 egg, beaten (for egg wash): Gives the bagel bites a beautiful golden sheen when baked.
- 4 oz cream cheese, cut into small cubes: The creamy, melty filling that makes these bites unforgettable.
- Everything bagel seasoning: Classic topping packed with flavor that brings a savory crunch.
- Sesame seeds: Optional topping adding nuttiness and texture.
- Poppy seeds: Another traditional bagel topping with a subtle crunch.
- Cinnamon sugar: For those who want a sweet twist on these savory bites.
How to Make High-Protein Bagel Bites Recipe
Step 1: Prepare Your Oven or Air Fryer
First things first, preheat your oven to 375°F (190°C) or, if you’re using an air fryer, set it to 350°F (175°C). This ensures the bagel bites will cook evenly and develop that perfect golden crust.
Step 2: Mix the Dry Ingredients
In a large bowl, combine the flour, baking powder, and salt. Whisking these ingredients together ensures your dough will have a consistent rise and balanced flavor throughout.
Step 3: Add the Greek Yogurt and Form Dough
Stir the Greek yogurt into the dry ingredients until a shaggy dough forms. This yogurt is what gives our bites that healthy protein lift and tender texture that’s impossible to resist.
Step 4: Knead the Dough
Lightly flour a clean surface and knead the dough for 1-2 minutes until smooth. Kneading develops the gluten slightly and helps the dough come together beautifully without being tough.
Step 5: Shape the Bagel Bites
Divide the dough into 8 equal pieces. Flatten each piece into a disc, place a cube of cream cheese in the center, then carefully wrap the dough around the filling, sealing the edges tightly to create a neat little ball. This step is key to keeping that creamy center perfectly encased.
Step 6: Add Egg Wash and Toppings
Brush each bagel bite with the beaten egg to lock in moisture and help the toppings adhere. Sprinkle generously with everything bagel seasoning, sesame seeds, poppy seeds, or cinnamon sugar to jazz up your bites with classic or creative flavors.
Step 7: Bake or Air Fry Until Golden
Arrange your bites on a lined baking sheet if baking, and cook for 20-22 minutes until they’re irresistibly golden. If using an air fryer, place them in the basket and cook for 10-12 minutes to get an extra crispy exterior. Let them cool slightly—then get ready to enjoy!
How to Serve High-Protein Bagel Bites Recipe

Garnishes
These bagel bites are fantastic as-is, but feel free to add a drizzle of honey or a smear of homemade pesto on the side for an extra burst of flavor. Fresh herbs like chives or dill can brighten up each bite beautifully, making your snack feel even more special.
Side Dishes
Serve your High-Protein Bagel Bites Recipe alongside a fresh green salad or a bowl of your favorite soup. The bites complement light, crisp sides wonderfully, making them ideal for a lunch, brunch, or casual dinner that’s quick but satisfying.
Creative Ways to Present
Try arranging your bagel bites on a platter with an assortment of dipping sauces like spicy mustard, creamy ranch, or a zesty yogurt dip. You could also assemble mini skewers by threading the bites with cherry tomatoes and olives for an elegant appetizer that’ll wow your guests.
Make Ahead and Storage
Storing Leftovers
If you have leftovers, store them in an airtight container in the refrigerator for up to 3 days. They maintain their fresh flavor and texture well, perfect for an easy grab-and-go snack or a quick breakfast option.
Freezing
To enjoy later, freeze the bagel bites by placing them on a baking sheet to freeze individually before transferring to a freezer-safe bag. They’ll keep for up to 2 months, letting you prep ahead without any compromise on taste.
Reheating
Reheat refrigerated or frozen bites by warming them in the oven at 350°F (175°C) for about 8-10 minutes until warmed through, or pop them in an air fryer for a few minutes to revive that fresh-baked crispness that makes every bite delightful.
FAQs
Can I substitute the Greek yogurt with something else?
You can use sour cream or a non-dairy yogurt alternative if needed, though plain Greek yogurt provides the best texture and protein boost for this recipe.
Is it necessary to use cream cheese filling?
The cream cheese gives these bagel bites their signature creamy center, but you could experiment with other fillings like shredded cheese, mashed avocado, or even a savory pesto for variety.
Can this recipe be made gluten-free?
Yes! Using a gluten-free all-purpose flour blend should work well, but be sure to check that your baking powder is gluten-free, too.
How spicy can I make these bagel bites?
For a little heat, try adding crushed red pepper flakes to the topping mix or a dash of cayenne pepper to the dough. It adds a lovely warmth without overpowering the cream cheese filling.
Are these suitable for meal prep or on-the-go snacks?
Absolutely! These bagel bites keep well in the fridge or freezer and are perfect for quick breakfasts, snacks, or lunchbox treats, making them a versatile addition to any meal plan.
Final Thoughts
There you have it—a delightfully simple, crowd-pleasing High-Protein Bagel Bites Recipe that delivers on taste, nutrition, and convenience all at once. Once you try making these little pockets of joy, I promise they’ll become a staple in your kitchen. So grab those ingredients and get ready to treat yourself and your loved ones to a snack that’s every bit as fun to make as it is to eat!
Print
High-Protein Bagel Bites Recipe
- Prep Time: 10 minutes
- Cook Time: 12 minutes (air fryer) or 22 minutes (oven)
- Total Time: 22 minutes (oven) or 22 minutes (air fryer, including preheat)
- Yield: 8 servings
- Category: Snack
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
These High-Protein Bagel Bites are a delicious and nutritious snack featuring a tender dough made from flour and Greek yogurt, filled with creamy cubes of cream cheese, and topped with a variety of flavorful seasonings. Perfectly baked or air fried to golden perfection, they offer a satisfying mix of textures and rich flavors in every bite.
Ingredients
Dough
- 1 cup all-purpose flour (or whole wheat flour)
- 2 tsp baking powder
- ½ tsp salt
- 1 cup plain Greek yogurt
Filling
- 4 oz cream cheese, cut into small cubes
Toppings
- 1 egg, beaten (for egg wash)
- Everything bagel seasoning
- Sesame seeds
- Poppy seeds
- Cinnamon sugar
Instructions
- Preheat Oven or Air Fryer: For oven baking, preheat the oven to 375°F (190°C) and line a baking sheet with parchment paper. For air frying, preheat the air fryer to 350°F (175°C) if needed.
- Mix Dry Ingredients: In a large bowl, whisk together the flour, baking powder, and salt until evenly combined.
- Add Yogurt: Add the plain Greek yogurt to the dry ingredients and mix thoroughly until a dough forms.
- Knead Dough: Transfer the dough to a lightly floured surface and knead for 1-2 minutes until the dough is smooth and elastic.
- Divide Dough: Divide the dough into 8 equal pieces to ensure uniform bagel bites.
- Fill Dough: Flatten each dough piece into a small disc, place a cube of cream cheese in the center, then wrap the dough around the cheese, sealing the edges to form a ball.
- Apply Egg Wash: Brush each bagel bite evenly with the beaten egg to help the toppings adhere and to promote browning.
- Add Toppings: Sprinkle your choice of everything bagel seasoning, sesame seeds, poppy seeds, or cinnamon sugar over each bagel bite.
- Bake or Air Fry: For oven baking, arrange the bagel bites on the prepared baking sheet and bake for 20-22 minutes until golden brown. For air frying, place the bagel bites in the air fryer basket and cook for 10-12 minutes until crispy and cooked through.
- Cool and Serve: Allow the bagel bites to cool slightly before serving. Enjoy them warm for the best flavor and texture.
Notes
- You can use either all-purpose flour or whole wheat flour depending on your preference for texture and nutrition.
- If you prefer a sweeter bite, opt for cinnamon sugar topping instead of savory toppings.
- Ensure the cream cheese cubes are well sealed inside the dough to prevent leakage during cooking.
- These bagel bites can be stored in an airtight container and reheated in the oven or air fryer for a crispy finish.
- To make them dairy-free, substitute cream cheese with a plant-based alternative and use a non-dairy yogurt.

