If you are craving a snack that is both satisfying and packed with protein, then this High-Protein Bagel Bites Recipe is about to become your new favorite treat. Imagine soft, golden bites of dough encasing creamy, tangy cream cheese, all topped with flavorful seasonings like everything bagel seasoning, sesame seeds, or a touch of cinnamon sugar. These bagel bites are perfect for a quick breakfast, a hearty snack, or a protein-rich appetizer. They blend simplicity with taste, making it incredibly easy to whip up something nourishing and delicious in just minutes.

Ingredients You’ll Need
This High-Protein Bagel Bites Recipe requires ingredients that are simple but play crucial roles in delivering the perfect texture and flavor. Each component is chosen to boost protein content while ensuring these bites remain soft, fluffy, and irresistibly tasty.
- All-purpose flour or whole wheat flour: Provides structure and a tender crumb to the dough, with whole wheat adding extra fiber.
- Baking powder: The secret to those wonderfully airy, light bites by helping the dough rise.
- Salt: Enhances overall flavor, balancing the creaminess of the cheese with the dough’s mild taste.
- Plain Greek yogurt: This ingredient adds moisture and protein plus a slight tanginess that makes each bite delightful.
- Egg (for egg wash): Creates a beautiful glossy finish on the baked bagel bites while helping the toppings stick.
- Cream cheese: The rich, creamy filling that contrasts perfectly with the soft, chewy dough.
- Everything bagel seasoning: Brings savory notes of garlic, onion, sesame, and poppy seed for that classic bagel experience.
- Sesame seeds: Adds a subtle nutty crunch and visual appeal.
- Poppy seeds: Provides a delicate texture boost with their tiny, crunchy pop.
- Cinnamon sugar: Offers a sweet twist if you want to switch things up and enjoy a hint of warmth and sweetness.
How to Make High-Protein Bagel Bites Recipe
Step 1: Preheat and Prep
Start by preheating your oven to 375°F (190°C) and lining a baking sheet with parchment paper to prevent sticking and promote even baking. If you prefer air frying, set your air fryer to 350°F (175°C). Preparing the baking environment first sets the stage for perfectly cooked bagel bites every time.
Step 2: Mix Dry Ingredients
In a large bowl, whisk together the flour, baking powder, and salt. This blends the leavening with the base flour evenly so your dough can rise properly without any clumps or uneven pockets.
Step 3: Add the Greek Yogurt
Stir in the plain Greek yogurt until the mixture transforms into a soft dough. Greek yogurt is the magic here – it keeps the dough moist and gives these bagel bites their signature protein boost.
Step 4: Knead the Dough
Turn the dough out onto a lightly floured surface and knead for 1 to 2 minutes until it’s smooth and a little elastic. This step ensures your dough has the right texture to hold the filling and bake up nicely.
Step 5: Divide and Fill
Divide the dough evenly into 8 pieces. Flatten each piece into a small disc, placing a cube of cream cheese right in the center. Then gently wrap the dough around the filling, pinching the edges securely to seal each bite into a neat ball.
Step 6: Egg Wash and Topping
Brush each bagel bite with the beaten egg. This is your ticket to that shiny golden crust while keeping the toppings firmly in place. Sprinkle generously with your choice of everything bagel seasoning, sesame seeds, poppy seeds, or even a sprinkle of cinnamon sugar if you want a sweet alternative.
Step 7: Bake or Air Fry
For the oven, arrange the bagel bites on the prepared baking sheet and bake for 20 to 22 minutes until they’re beautifully golden brown. If using an air fryer, place them in the basket and cook for 10 to 12 minutes until crisp and cooked through. Both methods produce delicious results — choose what’s most convenient for you.
Step 8: Cool and Enjoy
Allow your bagel bites to cool slightly before digging in – the cream cheese filling will be piping hot right out of the oven or air fryer. Enjoy them warm for the best flavor and texture experience.
How to Serve High-Protein Bagel Bites Recipe

Garnishes
Adding the right garnishes enhances the visual appeal and flavor profile of your High-Protein Bagel Bites Recipe. Fresh herbs like chopped chives or parsley bring a lively burst of color and brightness, while a light drizzle of olive oil can add an extra layer of richness. A sprinkle of flaky sea salt right before serving can sharpen the overall flavor too.
Side Dishes
When serving these bagel bites as a snack or light meal, pairing them with fresh-cut veggies like crunchy cucumber slices or juicy tomato wedges complements the creamy cheese. For a more substantial meal, consider a simple green salad loaded with mixed greens and a tangy vinaigrette that balances the richness of the bagel bites.
Creative Ways to Present
Get creative by serving the bagel bites on a rustic wooden board alongside small bowls holding additional toppings or dips like spicy mustard, herbed cream cheese, or honey mustard. Another fun idea is to thread the bagel bites on skewers for a portable and party-friendly presentation that guests will adore.
Make Ahead and Storage
Storing Leftovers
If you have leftovers, store them in an airtight container in the refrigerator for up to 3 days. This keeps the texture intact and ensures that when you reheat them, they taste just as delightful as fresh.
Freezing
To freeze, place the cooled bagel bites on a baking sheet in a single layer and freeze until solid, then transfer to a freezer-safe bag. They’ll keep well for up to 2 months, making this High-Protein Bagel Bites Recipe an excellent option for meal prepping or having a quick snack on hand.
Reheating
Reheat the bagel bites either in the oven at 350°F (175°C) for about 8 minutes or in an air fryer for 4 to 5 minutes to restore crispness. Avoid microwaving directly as it can make the dough a bit soggy and diminish the satisfying texture.
FAQs
Can I use a different type of cheese filling?
Absolutely! While cream cheese gives a creamy, classic taste, feel free to experiment with goat cheese, ricotta, or even shredded mozzarella depending on your flavor preferences.
Are these bagel bites suitable for a gluten-free diet?
This recipe calls for all-purpose or whole wheat flour, so it is not gluten-free. However, you can try substituting a gluten-free baking blend, but be aware the texture may vary slightly.
Can I make these without an oven?
Yes! Using an air fryer is a fantastic alternative, and it even reduces baking time. Just ensure the air fryer is preheated and cook until the bites are golden and crispy.
How can I make these bagel bites vegan?
To make a vegan version, substitute the Greek yogurt with a plant-based yogurt and replace the cream cheese with a vegan cream cheese. Use a flax egg or a similar egg replacer for the egg wash, though the shiny finish may be less pronounced.
What toppings work best for a sweet version?
Cinnamon sugar is the perfect topping for a sweet twist on this recipe. You can also try a sprinkle of chopped nuts or a drizzle of honey after baking for added flavor and texture contrast.
Final Thoughts
I can’t recommend enough giving this High-Protein Bagel Bites Recipe a whirl. It is one of those dishes that feels indulgent yet nourishing, perfect for busy mornings, quick snacks, or sharing with friends. Once you try them, you’ll see just how easily simple ingredients come together to create something so much more than the sum of their parts — soft, cheesy, flavorful bites that truly satisfy. Dive in and enjoy every bite!
Print
High-Protein Bagel Bites Recipe
- Prep Time: 10 minutes
- Cook Time: 12-22 minutes
- Total Time: 22 minutes
- Yield: 8 bagel bites
- Category: Snack
- Method: Baking
- Cuisine: American
- Diet: Low Fat
Description
These High-Protein Bagel Bites are a delicious and easy-to-make snack or breakfast option featuring a tender dough made with Greek yogurt, packed with protein, and filled with creamy cubes of cream cheese. Perfectly baked or air-fried for a golden, crispy exterior and soft, cheesy center, they’re topped with classic everything bagel seasoning, sesame seeds, poppy seeds, or cinnamon sugar for extra flavor.
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
- Everything bagel seasoning
- Sesame seeds
- Poppy seeds
- Cinnamon sugar
- 1 egg, beaten (for egg wash)
Instructions
- Preheat Oven or Air Fryer: For oven baking, preheat 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 your model requires preheating.
- Mix Dry Ingredients: In a large bowl, whisk together the flour, baking powder, and salt thoroughly to ensure an even rise and flavor distribution.
- Form Dough: Add the plain Greek yogurt to the dry ingredients and mix until a sticky dough forms. Use your hands or a spoon to combine all the ingredients well.
- Knead the Dough: Transfer the dough onto a lightly floured surface and knead gently for 1-2 minutes until the dough becomes smooth and elastic, making it easier to shape.
- Divide and Fill Dough: Divide the dough evenly into 8 pieces. Flatten each piece into a small disc and place a cube of cream cheese in the center.
- Shape Bagel Bites: Wrap the dough around the cream cheese cube, sealing the edges carefully to enclose the filling completely and form a ball-shaped bite.
- Apply Egg Wash and Add Toppings: Brush each bagel bite with the beaten egg to promote browning and help toppings adhere. Sprinkle your choice of everything bagel seasoning, sesame seeds, poppy seeds, or cinnamon sugar on top.
- Bake or Air Fry: For baking, arrange the bagel bites on the prepared baking sheet and bake in the oven for 20-22 minutes until golden brown. For air frying, place them in the air fryer basket and cook for 10-12 minutes until crispy and golden.
- Cool and Serve: Allow the bagel bites to cool slightly after cooking to set the cheese filling. Serve warm and enjoy these protein-rich, flavorful snacks.
Notes
- You can substitute all-purpose flour with whole wheat flour for a healthier option.
- If you want to keep these dairy-free, try using vegan cream cheese and yogurt alternatives.
- Feel free to mix different toppings to customize the flavor profiles.
- Ensure to seal the dough completely around the cream cheese to prevent leakage during cooking.
- These bagel bites are best enjoyed fresh but can be stored in the refrigerator for up to 2 days and reheated.

