As I rummaged through my kitchen pantry, I stumbled upon a bag of gluten-free flour, and a delicious idea struck me—High-Protein Bagel Bites! In just 15 minutes, I crafted these little gems that perfectly balance nutrition and comfort. With a chewy texture on the outside and a warm, creamy core filled with luscious cream cheese, they quickly became my go-to snack. Not only are they packed with protein, but they’re also air-fryer friendly, making them a breeze for busy mornings or that mid-afternoon hunger. The delightful crunch of Everything Bagel seasoning elevates each bite, leaving you craving more. Trust me, whether you’re a health enthusiast or just someone who loves homemade snacks, these bagel bites won’t disappoint. Ready to whip up these savory morsels? Let’s dive in!

Why Are These Bagel Bites Irresistible?
Quick preparation: Just 15 minutes from start to finish, these High-Protein Bagel Bites fit perfectly into any busy schedule.
Nutritious snacking: With around 8g of protein per bite, they’re a fantastic choice for those seeking healthy, homemade options.
Versatile delight: Customize your bagel bites with different fillings or seasoning to suit your taste preferences. Whether you prefer classic cream cheese or want to experiment with flavored options, the choice is yours!
Crowd-pleasing treat: Serve these bites at your next gathering, and watch them disappear—they’re sure to impress everyone at the table!
Air fryer perfection: Enjoy that delightful crunch without the guilt of deep frying. These bagel bites come out perfectly crispy and delicious every time!
If you love flavorful, healthy snacks, this is a recipe you’ll return to again and again. Pair them with a fresh Greek yogurt parfait for a nutritious breakfast or afternoon snack! For more delicious ideas, don’t miss my recipes for Steak Bites Garlic and Air Fryer Bites.
High-Protein Bagel Bites Ingredients
• Perfect your bites with this ingredient breakdown.
For the Dough
- Gluten-Free Flour – Choose a high-quality all-purpose blend to ensure a chewy texture.
- Baking Powder – Make sure it’s fresh to achieve that light rise.
- Unflavored Protein Powder – This boosts protein content; using flavored powder? Adjust sugar accordingly.
- Salt – Enhances the overall flavor profile of your bagel bites.
- Greek Yogurt – Use the thickest variety for a moist, protein-packed dough.
For the Filling
- Cream Cheese – For a creamy surprise in every bite; stick to block-style for easier filling.
For the Topping
- Everything But The Bagel Seasoning – Apply generously for that classic bagel flavor; it makes a delicious difference!
- Egg (optional) – An egg wash will improve color and help seasoning stick beautifully.
These High-Protein Bagel Bites are ready to be transformed into a delightful snack packed with flavor and nutrition!
Step‑by‑Step Instructions for High-Protein Bagel Bites
Step 1: Preheat the Air Fryer
Set your air fryer to preheat at 350°F (175°C). While it’s warming up, prepare your ingredients to ensure a smooth workflow. This will help create that perfect crispy exterior for your High-Protein Bagel Bites as they cook evenly.
Step 2: Mix the Dry Ingredients
In a large mixing bowl, combine your gluten-free flour, baking powder, unflavored protein powder, and salt. Whisk these together until well incorporated, ensuring there are no clumps. This mixture forms the backbone of your bagel bites, so take a moment to blend them thoroughly for the best texture.
Step 3: Combine with Greek Yogurt
Gradually fold in the Greek yogurt into your dry mixture. Stir until a sticky dough forms, which should take about 2-3 minutes of gentle mixing. If the dough feels too sticky, don’t hesitate to sprinkle in a touch more gluten-free flour. Aim for a smooth texture that’s still a bit tacky to the touch.
Step 4: Portion and Shape the Dough
Divide the dough into 10 equal parts, each weighing approximately 30g. Roll each piece into a smooth ball using your palms. This will be the base for your High-Protein Bagel Bites, so ensure each ball is nicely shaped for even cooking and a pleasant appearance.
Step 5: Add the Cream Cheese Filling
Flatten each dough ball gently to create a small disc. Spoon 1 teaspoon of cream cheese into the center and fold the edges over the filling to enclose it. Reshape the ball carefully, pinching the seams to keep the filling inside. These steps will ensure that every bite is bursting with creamy goodness!
Step 6: Prepare for Air Frying
Once shaped, brush each bagel bite lightly with an egg wash (if using) or spray with cooking oil. Generously sprinkle Everything But The Bagel seasoning on top to enhance flavor. This will give your High-Protein Bagel Bites that classic taste while also adding a delightful crunch.
Step 7: Air Fry the Bagel Bites
Carefully place the bagel bites in the preheated air fryer, ensuring there’s space between each to allow for even cooking. Air fry them for 5-6 minutes or until they turn a golden brown color. Keep an eye on them as they cook; you want that perfect balance of crispy outside and creamy inside.
Step 8: Cool and Serve
Once cooked, remove the bagel bites from the air fryer and let them cool for a couple of minutes. This brief resting time helps the cream cheese set slightly. Serve warm and enjoy the delightful blend of flavors and textures that make these High-Protein Bagel Bites an irresistible snack option!

High-Protein Bagel Bites Variations
Feel free to get creative with your bagel bites, elevating each one to match your cravings and dietary needs!
- Vegan Twist: Substitute Greek yogurt with coconut yogurt and cream cheese with dairy-free cream cheese for a plant-based delight.
- Sweet Treat: Mix in cinnamon and raisins into the dough for a sweet spin that kids will adore—think of a bagel bite dessert!
- Herb-Infused: Add fresh herbs like dill, chives, or basil to the dough for an aromatic flavor boost—it’s a treat for the senses!
- Spicy Kick: Incorporate minced jalapeños or a pinch of cayenne pepper in the dough for those who enjoy a little heat with their snacks.
- Savory Alternatives: Experiment with different fillings like whipped flavored cream cheese, such as garlic or herb, to elevate the flavor profile.
- Savory Topping: Instead of Everything But The Bagel seasoning, try a sprinkle of grated Parmesan or your favorite hard cheese before air frying.
- Pizza Style: Fill with mozzarella cheese and a dab of marinara sauce for a pizza-inspired bagel bite—a fun twist on this classic recipe!
If you’d like more delicious ideas to add to your snack repertoire, check out my recipe for Spinach Ricotta Rolls to whip up a creamy, cheesy treat after enjoying these bagel bites!
Storage Tips for High-Protein Bagel Bites
Room Temperature: Keep uneaten bagel bites in a cool, dry place for up to 1 day, but they’re best enjoyed fresh out of the air fryer.
Fridge: Store leftovers in an airtight container for up to 4 days. Reheat them in the air fryer at 350°F for a few minutes to restore their texture.
Freezer: Freeze the bagel bites in a single layer for up to 3 months. Once frozen, transfer to a zip-top bag for easy storage.
Reheating: For the best results, reheat from frozen in the air fryer at 350°F for about 8-10 minutes, ensuring a warm, gooey center in your High-Protein Bagel Bites.
Expert Tips for High-Protein Bagel Bites
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Fresh Ingredients: Ensure your baking powder is fresh for the best rise and texture; stale powder can lead to dense bagel bites.
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Dough Consistency: If the dough is too sticky, add a little more gluten-free flour until it achieves a smooth yet tacky feel.
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Perfect Frying: Don’t overcrowd the air fryer; leave space between each bagel bite to ensure they cook evenly and crisp up perfectly.
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Customize Your Filling: Experiment with different cream cheese flavors or even add herbs into the dough for a delightful twist in your High-Protein Bagel Bites!
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Storage Know-How: Store any leftovers in an airtight container for up to 4 days; for longer preservation, freeze them and reheat in the air fryer to restore their crispiness.
What to Serve with High-Protein Bagel Bites
Elevate your homemade high-protein snack by pairing it with these delicious accompaniments that will tantalize your taste buds.
- Fresh Fruit Salad: A colorful mix of seasonal fruits brings a refreshing sweetness that balances the savory bagel bites.
- Greek Yogurt Parfait: Layered with berries and granola, this parfait complements the creamy filling and adds a delightful crunch.
- Crispy Veggie Sticks: Carrot, cucumber, and bell pepper strips provide a satisfying crunch and refreshing contrast to each bite.
- Herbed Cream Cheese Dip: Enhance the creamy center with a herbed dip; it adds a fresh and flavorful twist.
- Spiced Roasted Chickpeas: Crunchy and protein-packed, these chickpeas add a delightful texture and spiced kick alongside your snacks.
- Homemade Hummus: Their creamy consistency pairs nicely with the bagel bites, providing a nutty flavor that brightens your snack time.
- Iced Herbal Tea: A refreshing drink to sip while enjoying bagel bites, enhancing the overall experience with a cool touch.
- Mini Shrimp Cocktail: If you’re entertaining, a shrimp cocktail adds a touch of elegance while complementing the bites perfectly.
Make Ahead Options
These High-Protein Bagel Bites are perfect for meal prep enthusiasts looking to save time during busy weekdays! You can prepare the dough up to 24 hours in advance by mixing the dry ingredients and combining them with Greek yogurt; simply wrap it tightly in plastic wrap and refrigerate. You can also shape the bagel bites, filling them with cream cheese, and refrigerate them for up to 3 days. To maintain their quality, avoid adding the seasoning until just before cooking. When you’re ready to enjoy, air fry them directly from the fridge for 5-6 minutes until golden brown, and you’ll have a delicious, wholesome snack with minimal effort!

High-Protein Bagel Bites Recipe FAQs
How do I select the best gluten-free flour for this recipe?
Absolutely! For the best results, choose a high-quality all-purpose gluten-free flour that contains xanthan gum. This will provide the structure needed for a chewy texture. Avoid blends that feel gritty, as they can affect the overall texture of your bagel bites.
What’s the best way to store leftover bagel bites?
I recommend storing leftovers in an airtight container in the fridge for up to 4 days. If you want them to last longer, you can freeze them for up to 3 months. Just be sure to reheat them in the air fryer at 350°F for a few minutes to restore that delightful crispiness!
Can I freeze the High-Protein Bagel Bites before cooking them?
Yes, you can! To freeze, shape your bagel bites but don’t air fry them first. Arrange them in a single layer on a parchment-lined baking sheet and freeze until solid. Then, transfer them to a zip-top bag for easy storage. When you’re ready to cook, simply air fry from frozen at 350°F for about 8-10 minutes, or until they’re golden and cooked through.
What if my dough is too sticky?
Very common! If you find your dough is a bit too sticky when mixing, simply sprinkle in a touch more gluten-free flour a little at a time until you achieve a smoother, manageable dough. This should only take a few extra minutes, so don’t stress about it—getting the consistency right is key to your bagel bites!
Are these bagel bites suitable for anyone with nut allergies?
Yes, as long as you select a gluten-free flour blend that doesn’t contain nuts, these High-Protein Bagel Bites should be safe for those with nut allergies. However, always double-check the labels to be sure there are no cross-contaminations.

Savory High-Protein Bagel Bites Ready in Just 15 Minutes
Ingredients
Equipment
Method
- Preheat the Air Fryer to 350°F (175°C).
- Mix the dry ingredients: gluten-free flour, baking powder, protein powder, and salt in a large bowl.
- Combine Greek yogurt with the dry mixture until a sticky dough forms.
- Divide the dough into 10 equal parts and roll each into a smooth ball.
- Flatten each ball, add 1 teaspoon of cream cheese, and reshape it to enclose the filling.
- Brush each bagel bite with egg wash or spray with cooking oil, then sprinkle with seasoning.
- Air fry for 5-6 minutes until golden brown.
- Let cool for a couple of minutes, then serve warm.

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