As I stood in my kitchen, the scent of toasted bagels wafted through the air, sparking an idea: why not create a high-protein version? That led to my new favorite snack—Quick and Easy High-Protein Bagel Bites! These little wonders are not only gluten-free but also a breeze to whip up in under 15 minutes. Whether you’re rushing out the door in the morning or craving a satisfying afternoon treat, these bite-sized delights deliver a creamy center surrounded by a golden, crispy exterior. Packed with protein and nutrients, they are the perfect guilt-free indulgence. So, who’s ready to transform snack time into a healthy and delicious occasion? Let’s get cooking!

Why are High-Protein Bagel Bites amazing?
Nutritional Boost: Packed with protein, these bagel bites are a smart choice for health-conscious snackers looking to fuel their day.
Quick Prep: Ready in just 15 minutes, they make busy mornings seamless while delivering satisfying flavor without the wait.
Gluten-Free Delight: Enjoy these delicious bites guilt-free, as they’re gluten-free and cater to various dietary preferences.
Versatile Filling: Customize with flavored cream cheeses or spices to keep every batch exciting.
Perfect Snack Size: Ideal for on-the-go munching or a quick pick-me-up, they pair perfectly with a refreshing yogurt parfait or fresh veggie sticks. Discover even more easy snack ideas like our Wrapped Mozzarella Bites or No-Bake Peanut Butter Energy Bites to elevate your snack game!
High-Protein Bagel Bites Ingredients
• Get ready to whip up these delightful snacks!
For the Dough
- Gluten-Free Flour – Provides structure and texture; opt for an all-purpose blend with xanthan gum for the best consistency.
- Baking Powder – Ensures your bagel bites rise beautifully without yeast; always check its freshness for optimal effectiveness.
- Unflavored Protein Powder – Boosts the protein content without altering the flavor; if using a flavored option, reduce any additional sweeteners to balance.
- Salt – Enhances overall flavor; just a pinch balances the sweetness from the yogurt and cream cheese.
- Greek Yogurt – Acts as a moisture and protein powerhouse; choose thick yogurt for an ideal dough texture.
For the Filling
- Cream Cheese – Adds a rich, creamy filling; using block-style cream cheese chilled from the fridge makes it easier to handle.
For the Topping
- Everything But The Bagel Seasoning – Infuses authentic bagel flavor; sprinkle generously for an extra crunch and taste boost.
- Egg (optional) – Use for an egg wash to achieve a shiny finish and help the seasoning adhere.
Now you have everything ready to create your High-Protein Bagel Bites! Let’s dive into the fun of transforming these ingredients into a delightful snack.
Step‑by‑Step Instructions for High-Protein Bagel Bites
Step 1: Preheat Your Air Fryer
Begin by preheating your air fryer to 350°F (175°C). This step is crucial as it ensures that your High-Protein Bagel Bites cook evenly and become perfectly golden and crispy on the outside. While the air fryer warms up, gather all your ingredients and equipment to streamline the preparation process.
Step 2: Mix Dry Ingredients
In a medium mixing bowl, combine gluten-free flour, baking powder, unflavored protein powder, and a pinch of salt. Use a whisk to blend the dry ingredients thoroughly until the mixture is uniform in color and free of lumps. This step is essential for ensuring that your High-Protein Bagel Bites have a consistent texture throughout.
Step 3: Incorporate Greek Yogurt
Add the thick Greek yogurt to your dry ingredient mixture. Using a sturdy spatula or your hands, mix everything together until a sticky dough forms. Be careful not to overmix, as this can toughen the bites. The dough should be cohesive but slightly tacky, ready to be shaped into delightful bites.
Step 4: Shape the Dough
Divide the sticky dough into 10 equal pieces. Roll each piece into a ball using your palms, ensuring they are smooth. After rolling, flatten each ball gently to form a small disc. This will create a base for your filling, making it easy to shape your High-Protein Bagel Bites later.
Step 5: Add the Cream Cheese Filling
Spoon about 1 teaspoon of cream cheese into the center of each flattened dough disc. Carefully fold the edges of the dough over the cream cheese, pinching them tightly to seal in the filling. This ensures that your bagel bites will have a deliciously creamy center that surprises you with each bite.
Step 6: Egg Wash and Season
If using, beat an egg in a small bowl and brush the top of each sealed bagel bite with the egg wash. This gives them a beautiful golden color as they cook. Sprinkle a generous amount of Everything But The Bagel seasoning on top for that authentic bagel flavor and delightful crunch you’ll love.
Step 7: Air Fry the Bagel Bites
Carefully place the prepared bagel bites in the preheated air fryer basket, ensuring they are spaced apart to allow for even cooking. Air fry them for 5-6 minutes, or until they turn golden brown and emit a delicious aroma. Keep an eye on them toward the end to prevent overcooking!
Step 8: Cool Before Serving
Once done, carefully remove the High-Protein Bagel Bites from the air fryer and let them cool for a few minutes. This step is important for safety and allows the filling to set slightly. Serve warm and enjoy these tasty bites guilt-free, packed with protein and flavor!

Expert Tips for High-Protein Bagel Bites
- Mixing Matter: Avoid overmixing the dough; mix until just combined to keep your High-Protein Bagel Bites tender and light.
- Flour Selection: Choose a gluten-free flour blend that contains xanthan gum for optimal structure—this will give your bites that authentic bagel texture.
- Cream Cheese Handling: Use cold block-style cream cheese for easier handling and to prevent it from melting too quickly during cooking.
- Air Fryer Spacing: Ensure there’s space between each bagel bite in the air fryer basket; overcrowding can lead to uneven cooking and soggy bites.
- Topping Generosity: Don’t skimp on the Everything But The Bagel seasoning; a generous sprinkle enhances both the flavor and crunch of your bites!
Make Ahead Options
These High-Protein Bagel Bites are perfect for meal prep fans! You can prepare the dough and shape the bites up to 24 hours in advance; simply cover them tightly with plastic wrap and refrigerate to maintain freshness. To ensure they stay delicious, it’s essential to seal them well to prevent drying out. When you’re ready to cook, brush them with the egg wash, sprinkle with Everything But The Bagel seasoning, and air fry them straight from the fridge for about 5-6 minutes. For longer storage, you can freeze the unbaked bites for up to 3 months—just pop them in the air fryer directly from frozen, adding a minute or two to the cooking time. Enjoy the convenience of a quick snack anytime!
How to Store and Freeze High-Protein Bagel Bites
Fridge: Store your High-Protein Bagel Bites in an airtight container in the fridge for up to 4 days to maintain their freshness and flavor.
Freezer: For longer storage, freeze the bagel bites individually on a baking sheet before placing them in a freezer-safe bag or container. They can be kept for up to 3 months.
Reheating: To reheat, air fry directly from frozen at 350°F for about 8–10 minutes or until heated through and crispy. Enjoy delicious bites even after freezing!
Wrapping: For best preservation, wrap each bagel bite in plastic wrap before freezing to prevent freezer burn and maintain taste.
What to Serve with High-Protein Bagel Bites
Elevate your snack experience by pairing these delicious bites with refreshing sides and uplifting beverages.
- Fresh Fruit Salad: Bursting with sweetness, a colorful fruit salad provides a light contrast to the savory bagel bites.
- Creamy Hummus Dip: Smooth and rich, hummus enhances the protein-packed bites with an extra layer of flavor and nutrition.
- Veggie Sticks: Crunchy carrots, bell peppers, and cucumbers add a delightful crunch, promoting a satisfying balance of textures alongside the bites.
- Greek Yogurt Parfait: Layered with berries and a drizzle of honey, this parfait complements the bagel bites with creaminess and natural sweetness.
- Protein Smoothie: Whip up a fruity protein smoothie to make your snack time even more fulfilling, infusing it with vitamins and energy.
- Crispy Kale Chips: For a crunchy side, bake kale chips seasoned with salt; their earthy flavor pairs well with the cheesy filling of the bites.
- Chilled Sparkling Water: Add a refreshing twist by serving your bagel bites with sparkling water infused with lemon or lime, enhancing your snack experience.
- Chocolate-Covered Almonds: Treat yourself to a handful of these sweet and nutty bites for a delightful dessert that rounds out the meal perfectly.
- Savory Soup: A warm bowl of tomato or butternut squash soup makes for a comforting combo, complementing the High-Protein Bagel Bites beautifully.
High-Protein Bagel Bites Variations
Customize your High-Protein Bagel Bites to suit your taste buds and dietary preferences—your kitchen will be bursting with delicious, vibrant flavors!
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Dairy-Free: Swap Greek yogurt for thick coconut yogurt for a creamy, non-dairy version that’s just as satisfying.
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Savory Fillings: Experiment with flavored cream cheeses like scallion or chive to add an extra layer of savory delight to your bites.
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Sweet Twist: Mix in cinnamon and raisins into the dough for a delectable sweet spin, perfect for those who enjoy a hint of dessert in their snacks.
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Spicy Kick: Add diced jalapeños or a pinch of red pepper flakes to the filling for a zesty bite that tantalizes the taste buds.
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Herb Infusion: Incorporate fresh herbs like rosemary or dill into the dough for a fragrant and flavorful twist with every bite.
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Crunchy Topping: Top your bagel bites with crushed nuts or seeds along with the Everything But The Bagel seasoning for extra texture and nutrition.
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Cheesy Goodness: Try using a variety of cheeses such as cheddar or pepper jack in the filling for a melty surprise that will please any cheese lover.
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Protein Power-Up: Boost the protein content further by adding finely chopped cooked chicken or turkey to the cream cheese filling—perfect for a heartier snack.
Whether you opt for a sweet or savory variation, these High-Protein Bagel Bites are versatile enough to go with your mood! And while you’re at it, why not serve them alongside a refreshing yogurt parfait or try our tasty Golden Cheesy Mashed Potato Puff Bites for an unforgettable meal?

High-Protein Bagel Bites Recipe FAQs
What type of gluten-free flour should I use?
I recommend using an all-purpose gluten-free flour that contains xanthan gum. This will provide the structure and texture needed for your High-Protein Bagel Bites. Be sure to check the package for any additional ingredients or substitutes that may be present!
How long can I store High-Protein Bagel Bites in the fridge?
You can store them in an airtight container in the fridge for up to 4 days. Just make sure they are completely cooled before sealing them to maintain their crispy texture!
Can I freeze my High-Protein Bagel Bites? If so, how?
Absolutely! To freeze them, place the cooled bagel bites on a baking sheet in a single layer, and freeze until solid. This prevents them from sticking together. After they are frozen, transfer them to a freezer-safe bag or container, where they will keep well for up to 3 months.
What should I do if my bagel bites come out too tough?
If your bagel bites are tough, it could be due to overmixing the dough. Be sure to mix just until combined, and consider using a thicker Greek yogurt to help maintain moisture. Always check that your baking powder is fresh, as old ingredients can affect the texture.
Are High-Protein Bagel Bites safe for pets or certain allergies?
While these bagel bites are delicious for humans, they contain ingredients like cream cheese and may pose a risk to pets like dogs or cats. Additionally, they’re vegetarian but not suitable for those with dairy allergies unless you use a dairy-free cream cheese alternative. Always check ingredient labels for allergens before serving anyone with dietary restrictions.
How can I reheat frozen High-Protein Bagel Bites?
To reheat your frozen High-Protein Bagel Bites, place them directly into a preheated air fryer at 350°F. Cook for about 8–10 minutes, or until they are heated through and the exterior becomes crispy again. Enjoy them as if they were freshly made!

Savor These High-Protein Bagel Bites: Quick & Guilt-Free!
Ingredients
Equipment
Method
- Preheat your air fryer to 350°F (175°C).
- In a medium mixing bowl, combine gluten-free flour, baking powder, unflavored protein powder, and a pinch of salt. Whisk until uniform.
- Add Greek yogurt to the dry ingredients and mix until a sticky dough forms.
- Divide the dough into 10 equal pieces, roll into balls, and flatten them into small discs.
- Spoon about 1 teaspoon of cream cheese into the center of each disc, fold edges over, and pinch to seal.
- If using, brush the tops with beaten egg and sprinkle with Everything But The Bagel seasoning.
- Place bagel bites in the air fryer and cook for 5-6 minutes until golden brown.
- Let cool for a few minutes before serving warm.

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