As I stood shaking the seasoning over the dough, I felt a wave of motivation wash over me—snacks don’t have to come in a crinkly package. Enter my High-Protein Bagel Bites, a delicious solution to satisfy those cravings without sacrificing nutrition. In just 15 minutes, these gluten-free bites deliver a chewy exterior enveloping a rich, creamy center, making them perfect for busy mornings or unexpected snack attacks. Not only do they pack protein to fuel your day, but they’re also quick to whip up, transforming healthy eating into a joyful experience. Ready to elevate your snack game and indulge without guilt? Trust me, your taste buds are in for a delightful surprise!

Why Are These Bagel Bites a Must-Try?
Simplicity at its Core: You only need 15 minutes to whip up these high-protein bagel bites, making them a perfect choice for anyone short on time.
Irresistible Flavor: With a creamy center and seasoned exterior, each bite bursts with flavor that rivals your favorite gourmet snacks.
Nutritious Fuel: Packed with protein and minimal sugar, they make a healthy snack option that doesn’t compromise on taste, ideal for busy mornings or afternoon cravings.
Versatile Pairing: Serve them with fresh fruit or a yogurt parfait for a satisfying meal, or enjoy them solo for a quick bite that feels indulgent.
Family-Friendly Appeal: Even picky eaters will love the familiar bagel taste, ensuring everyone will come back for seconds.
Don’t forget to check out my Garlic Chicken Bites for another healthy and delicious snack idea!
High-Protein Bagel Bites Ingredients
For the Dough
• Gluten-Free Flour – This is your base ingredient providing structure; opt for a smooth all-purpose blend for the best texture.
• Baking Powder – A crucial leavening agent that allows the bagel bites to rise; make sure it’s fresh for optimal fluffiness.
• Unflavored Protein Powder – Boosts the protein content without changing the taste; if you use a flavored one, cut back on added sweeteners.
• Salt – Essential for enhancing the overall flavor; a little goes a long way.
• Plain Unsweetened Greek Yogurt – Adds moisture and a dose of protein; use thicker varieties to avoid sogginess.
For the Filling
• Cream Cheese – The star of the filling, providing a rich, creamy center; block-style cream cheese works best for easy handling.
For the Finish
• Egg (for brush) – Gives a lovely shiny finish and helps the seasoning adhere; while optional, I recommend it for an appetizing look.
• Everything But The Bagel Seasoning – Infuses those classic bagel vibes; don’t be shy with this—it makes all the difference in flavor!
These high-protein bagel bites are not just a snack; they’re a savory journey that promises to elevate your kitchen adventures while keeping your health in check!
Step‑by‑Step Instructions for High-Protein Bagel Bites
Step 1: Preheat the Air Fryer
Begin by preheating your air fryer to 350°F (175°C). This step is crucial as it ensures a golden, crispy exterior for your high-protein bagel bites. While the air fryer heats, set up your ingredients to keep the cooking process smooth and efficient.
Step 2: Mix the Dry Ingredients
In a large mixing bowl, combine 1 cup of gluten-free flour, 1 tablespoon of baking powder, 1 scoop of unflavored protein powder, and a pinch of salt. Stir these dry ingredients together until fully blended, ensuring even distribution. This mixture forms the base for your bagel bites, so precision and thorough mixing are key.
Step 3: Incorporate the Wet Ingredients
Next, add 1 cup of plain unsweetened Greek yogurt to the dry ingredients. Using a fork, gently mix until the dough starts to come together. Once it’s too thick to stir, switch to your hands, kneading lightly until a sticky, workable dough forms. This texture is what gives your bagel bites their chewy goodness.
Step 4: Divide the Dough
Once your dough is ready, divide it into 10 equal pieces, aiming for about 30 grams each. Shape these pieces into round balls and let them rest briefly. This step allows the dough to relax, making it easier to flatten and mold into the classic bagel shape.
Step 5: Form the Bagel Bites
Flatten each dough ball into a disc, then place about 1 teaspoon of cream cheese in the center of each. Carefully fold the edges over the filling and roll gently to seal. This technique encases the creamy center within the chewy dough and is essential for that delightful bite.
Step 6: Prepare for Cooking
Brush each bagel bite lightly with a beaten egg for a shiny finish, or spray with a bit of oil. Generously sprinkle with Everything But The Bagel seasoning, ensuring you don’t miss any parts of your high-protein bagel bites. This step enhances flavor and makes them visually appealing.
Step 7: Air Fry the Bagel Bites
Place the prepared bagel bites in the air fryer basket, making sure to leave some space between each one to allow for even cooking. Air fry at 350°F (175°C) for 5 to 6 minutes, or until they turn a lovely golden-brown color. The timer is crucial for achieving the perfect chewy texture without undercooking.
Step 8: Cool and Serve
Once cooked, remove the bagel bites from the air fryer and let them cool for a few minutes. Be cautious, as the filling will be hot. After cooling slightly, they’re ready to enjoy! The combination of crispy exterior and creamy center will surely satisfy your snack cravings.

How to Store and Freeze High-Protein Bagel Bites
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Room Temperature: Store any leftover bagel bites in a cool, dry place for up to 1 day. Wrap them in paper towels to keep moisture at bay.
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Fridge: For longer freshness, keep the bagel bites in an airtight container in the fridge for up to 4 days. Line the container with a paper towel to absorb any excess moisture.
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Freezer: These high-protein bagel bites freeze beautifully! Place them in a freezer-safe bag or container for up to 3 months. Be sure to separate any layers with parchment paper.
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Reheating: To enjoy them warm, reheat from frozen in the air fryer at 325°F for about 4-5 minutes. This will ensure they stay crispy on the outside and creamy inside!
Make Ahead Options
These High-Protein Bagel Bites are perfect for meal prep enthusiasts looking to save time during busy days! You can prepare the dough up to 24 hours in advance by mixing the dry ingredients and incorporating the Greek yogurt, then wrapping it tightly in plastic wrap and refrigerating it. Additionally, you can shape the bagel bites filled with cream cheese and freeze them for up to 3 months; just place them in a single layer on a baking sheet before transferring to an airtight container. When you’re ready to enjoy, simply air fry from frozen at 350°F (175°C) for 5-6 minutes. This way, you will have delicious and nutritious snacks ready to go whenever the cravings strike—just as satisfying as freshly made!
What to Serve With High-Protein Bagel Bites
Elevate your snacking experience with delightful pairings that complement these protein-packed bites.
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Creamy Hummus: Spread a layer of creamy hummus for a flavorful dip that adds richness and pairs beautifully with the chewy texture.
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Fresh Fruit Salad: A mix of seasonal fruits provides a refreshing contrast, lifting your meal with vibrant colors and natural sweetness.
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Greek Yogurt Parfait: Layer Greek yogurt with berries and granola for a wholesome balance, transforming your bagel bites into a nourishing breakfast.
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Veggie Sticks: Crisp carrot, celery, and bell pepper sticks offer a satisfying crunch, perfect for dipping into your favorite spread.
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Avocado Toast: Top gluten-free bread with ripe avocado and seasonings; it adds creaminess and healthy fats that meld delightfully with your bagel bites.
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Sparkling Water: Refreshing sparkling water with a hint of citrus cleanses your palate between bites, making each taste a crisp, delightful moment.
Pairing these high-protein bagel bites with complementary flavors and textures creates a well-rounded meal that satisfies every craving!
High-Protein Bagel Bites Variations
Feel free to get creative with these bagel bites and customize them to your taste!
- Dairy-Free: Substitute Greek yogurt with coconut yogurt and use dairy-free cream cheese for a delicious alternative.
- Traditional Flour: If gluten isn’t a concern, swap gluten-free flour for regular all-purpose flour to achieve a similar texture.
- Sweet Twist: Add cinnamon and raisins to the dough for a delightful sweet variation, perfect for breakfast!
- Herb Infusion: Mix in dried herbs like dill or chives to the dough for a savory flavor boost that’s simply irresistible.
- Spicy Kick: Incorporate a dash of red pepper flakes or cayenne into the dough to spice things up and wake up your taste buds.
- Veggie-Packed: Fold in finely chopped spinach or bell peppers with the cream cheese filling for extra nutrition and color.
- Cheesy Delight: Swap the cream cheese for a flavored cheese spread or even mozzarella for a gooey, cheesy center.
- Mini Bagels: Shape the dough into miniature rings for bite-sized treats that are perfect for dipping in your favorite sauces!
Whether you’re looking to change up the flavor profile or accommodate special dietary needs, these variations will keep your snacking routine exciting. For additional creative ideas, explore my Cornbread Waffle Bites or try my Cinnamon Roll Protein Bites for a sweet treat!
Expert Tips for High-Protein Bagel Bites
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Check Yogurt Consistency: Ensure the Greek yogurt isn’t watery; straining it helps maintain the perfect dough texture and avoids sogginess.
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Avoid Overcrowding: Place bagel bites in the air fryer basket with space between them. This ensures even cooking and achieves that coveted golden-brown finish.
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Use Fresh Baking Powder: For best results, check the expiry date on your baking powder. Freshness is key to getting those bagel bites to rise beautifully.
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Mind the Cream Cheese: Use block-style cream cheese for easy handling. If it’s too soft, it may not hold up well during cooking.
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Experiment with Flavors: Don’t hesitate to adjust the Everything But The Bagel seasoning to your taste! Adding herbs or spices can elevate your high-protein bagel bites further.

High-Protein Bagel Bites Recipe FAQs
What type of gluten-free flour should I use?
When selecting gluten-free flour, opt for a smooth all-purpose blend that mimics traditional flour without a gritty texture. Brands like Bob’s Red Mill or King Arthur have great options. Always check for freshness, as out-of-date flour can affect the rise and texture of the bagel bites.
How should I store leftover High-Protein Bagel Bites?
To enjoy your bagel bites at their best, store them in an airtight container in the fridge for up to 4 days. I recommend lining the container with a paper towel to absorb excess moisture, keeping the bites fresh and chewy. If you’d like to keep them longer, you can freeze them—just wrap each bite individually with plastic wrap before placing them in a freezer-safe bag.
Can I freeze these bagel bites?
Absolutely! These high-protein bagel bites freeze wonderfully. Place them in a freezer-safe container or bag, ensuring to separate any layers with parchment paper to avoid sticking. They will stay fresh for up to 3 months. When you’re ready to eat, simply reheat from frozen in the air fryer at 325°F for about 4-5 minutes for optimal crispiness.
What if my dough is too sticky to work with?
If your dough feels excessively sticky, it may be due to the moisture content of your Greek yogurt. To remedy this, lightly dust your working surface and hands with additional gluten-free flour as you knead. If it remains sticky, consider adding a touch more flour, a teaspoon at a time, until you achieve the desired texture without compromising the moisture.
Can my pets have the bagel bites?
While the ingredients in these high-protein bagel bites are generally safe for humans, they are not suitable for pets. Ingredients like cream cheese should be avoided for dogs and cats due to their digestive sensitivities. Always check with your veterinarian if you have any doubts about sharing human food with your furry friends.
What if I want to modify the recipe for dietary needs?
If you’re looking to adapt the recipe, you can swap out Greek yogurt for coconut yogurt to make it dairy-free, and use dairy-free cream cheese for the filling. Additionally, if gluten isn’t a concern, you can try using regular all-purpose flour while adjusting the amount to maintain the right dough consistency. Don’t hesitate to explore flavor variations—adding cinnamon and raisins for a sweet version or fresh herbs for something savory can take these bites to another level!

High-Protein Bagel Bites That Make Snacking Feel Gourmet
Ingredients
Equipment
Method
- Preheat your air fryer to 350°F (175°C).
- In a large mixing bowl, combine the dry ingredients: gluten-free flour, baking powder, protein powder, and salt.
- Add Greek yogurt to the dry ingredients and mix lightly until the dough forms.
- Divide the dough into 10 equal pieces and shape into round balls.
- Flatten each ball, place cream cheese in the center, and fold over to seal.
- Brush each bagel bite with beaten egg and sprinkle with Everything But The Bagel seasoning.
- Air fry for 5 to 6 minutes or until golden brown.
- Cool slightly before serving to enjoy the crispy exterior and creamy center.
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