There’s a certain thrill when you realize that creating a batch of delicious, protein-packed bagels is simpler than you ever imagined. Picture this: warm, chewy bagels fresh from your kitchen, bursting with the goodness of Greek yogurt and loaded with 18 grams of protein each. Perfect for those busy mornings or lazy weekend brunches, these High Protein Greek Yogurt Bagels come together in just 30 minutes with minimal ingredients and zero fuss.
During a recent grocery run, I found myself staring at the endless options of bland, store-bought bagels—wondering if I could whip up something better at home. Enter this easy, gluten-free recipe that transforms the humble bagel into a nutritional powerhouse. Whether you’re craving a classic breakfast with cream cheese or a savory snack with avocado, these versatile bagels will leave everyone impressed. So, let’s roll up our sleeves and dive into a world of delightful flavors and satisfying textures!

Why Choose Protein Bagels for Breakfast?
Quick and Easy: You’ll love how this recipe requires only five simple ingredients and takes just 30 minutes from start to finish.
High Protein Boost: With an impressive 18 grams of protein per bagel, you can fuel your mornings without sacrificing flavor.
Gluten-Free Goodness: Perfect for gluten-sensitive eaters, these bagels can be enjoyed by everyone without worry.
Versatile Customization: Experiment with various toppings and mix-ins to cater to your taste preferences—whether savory or sweet.
Crowd-Pleaser: Family and friends will be amazed when you serve these homemade delights for breakfast or brunch.
Protein Bagel Ingredients
For the Bagels
• 1 cup gluten-free all-purpose flour – Provides structure and texture; substitute with all-purpose flour if gluten isn’t a concern.
• 1 tsp baking powder – Essential for achieving that perfect bagel lift and texture.
• Pinch of salt – Enhances flavor and balances the sweetness from other ingredients.
• 1 cup plain unsweetened Greek yogurt – Adds moisture and a whopping protein boost; can be replaced with cottage cheese blended until smooth.
For Topping
• Everything But The Bagel Seasoning – A fantastic blend to elevate your bagels’ flavor; you can also switch it with sesame seeds or your favorite spice mix.
Enjoy making these delicious protein bagels that everyone will love!
How to Make Protein Bagels
Combine Ingredients: In a large bowl, mix the gluten-free flour, baking powder, and pinch of salt until well combined. This dry mixture forms the base for your chewy bagels.
Incorporate Yogurt: Stir in the Greek yogurt, blending until a cohesive dough forms. It should be slightly sticky but manageable; don’t fret if it’s a bit messy!
Shape the Dough: Divide the dough into two equal parts, then shape each into a smooth ball on a lightly floured surface. Gentle handling will help maintain the bagels’ structure.
Form Bagels: Roll each ball into a rope, pinching the ends together to create the classic bagel shape. This rolling technique enhances the chewiness—just what we want!
Preheat the Air Fryer: Set your air fryer to 350°F, letting it warm up for about 5 minutes while you prepare the bagels for cooking.
Prepare for Cooking: Lightly spray the bagels with non-stick spray or drizzle olive oil over them. Sprinkle your Everything But The Bagel Seasoning generously on top for that tasty crunch.
Cook the Bagels: Place the bagels in the air fryer and cook for about 8 minutes, until they’re golden brown. For extra crispiness, flip the bagels and air fry for an additional 2-3 minutes.
Optional: Serve warm with your favorite toppings like cream cheese or avocado.
Exact quantities are listed in the recipe card below.

Expert Tips for Protein Bagels
Perfect Your Dough: Adjust flour for desired texture; if the dough is too sticky, add a tablespoon at a time until manageable for shaping.
Air Fryer Secrets: Ensure even cooking by not overcrowding the basket; allow space between bagels for optimal air circulation and crispiness.
Oven Alternative: If baking, preheat to 350°F and use parchment paper for an easy release and even baking for approximately 20-25 minutes.
Customize Toppings: Experiment with seasonings—try garlic powder or cheese instead of Everything But The Bagel to personalize your protein bagels.
Baking Time: Keep an eye on your bagels during cooking; every appliance varies slightly, and you want that golden, crispy finish!
How to Store and Freeze Protein Bagels
Fridge: Keep your protein bagels in an airtight container in the refrigerator for up to 3 days to retain freshness and flavor.
Freezer: For longer storage, individually wrap bagels in plastic wrap and place them in a freezer-safe bag; they can be frozen for up to 3 months.
Reheating: To enjoy them again, simply toast the bagels until warmed through and crispy. They’re delightful with your favorite toppings!
Room Temperature: If you plan to eat them within a day, you can store your protein bagels at room temperature in a sealed container, but avoid longer storage to maintain quality.
Variations & Substitutions for Protein Bagels
Explore exciting twists you can add to your protein bagels for a truly personalized experience in every bite!
Dairy-Free: Substitute Greek yogurt with almond or coconut yogurt for a dairy-free version while still maintaining that delicious creaminess.
You won’t lose the moisture or protein content, making for a perfect alternative!Flavored Yogurt: Experiment with flavored Greek yogurt, such as vanilla or honey, to add a hint of sweetness and uniqueness to each bagel.
This simple swap can completely change the flavor profile, turning your bagels into a delightful treat!Herb-Infused: Incorporate chopped fresh herbs like dill, chives, or parsley directly into the dough for aromatic, herbaceous bagels.
It brings an incredible burst of freshness that pairs beautifully with savory toppings.Cheesy Delight: Add shredded cheese like cheddar or mozzarella into the dough for an indulgent twist and gooey texture.
These cheesy bagels are irresistible right out of the air fryer or oven!Sweet Sprinkle: Top your bagels with a mix of cinnamon and sugar for a delightful sweet snack or dessert option.
This sweet variation can be perfect with a smear of cream cheese or simply enjoyed on their own.Nutty Crunch: Fold in chopped nuts or seeds, like walnuts or flaxseeds, for added texture and healthy fats.
This not only enhances the flavor but also amps up the nutritional value of your bagels.Spicy Kick: Mix in a pinch of crushed red pepper flakes or jalapeño bits for some heat in your bagels.
For those who love spice as a flavor enhancer, this twist will awaken your taste buds!Savory Toppings: Instead of the classic seasoning, try za’atar or sumac for a Middle Eastern vibe that’s simply delightful.
This little change can transform the bagels and elevate your brunch gathering!
What to Serve with Protein Bagels?
Building the perfect breakfast or brunch is all about balance, and these delicious bagels offer a fantastic base for your culinary creativity.
Creamy Avocado Spread: The rich, buttery texture of avocado brings a delightful creaminess that complements the chewy bagels. Top with a sprinkle of salt and pepper for a simple yet luxurious touch.
Smoked Salmon: This classic pairing introduces a smoky, savory element that elevates your bagel to gourmet status. Layer with cream cheese and capers for a stunning brunch treat.
Fresh Fruit Salad: A bright and colorful mix of seasonal fruits adds a refreshing sweetness to your meal. This contrast balances the hearty, protein-rich bagel beautifully.
Greek Yogurt with Honey: For a sweet twist, enjoy a bowl of Greek yogurt drizzled with honey. It echoes the yogurt in the bagel while providing a lovely creamy texture and a touch of sweetness.
Herbed Cream Cheese: Whip up a quick herbed cream cheese spread to enjoy with your bagels. The flavors of fresh herbs provide a zesty pop, and the creamy texture ties everything together.
Breakfast Sandwich Assembly: Stack your bagel with eggs, cheese, and your favorite breakfast meat for a filling sandwich. It’s a satisfying way to kick-start your day!
Indulge in these delightful pairings, and watch as your morning routine transforms into a feasting experience!
Make Ahead Options
These Protein Bagels with Greek Yogurt are a fantastic option for meal prep, perfect for busy mornings! You can prepare the dough up to 24 hours in advance by mixing the dry ingredients and Greek yogurt, then covering it tightly with plastic wrap and refrigerating it. To maintain the bagels’ chewy texture, shape them into bagels only right before cooking. When you’re ready to enjoy, simply pull the dough from the fridge, shape your bagels, and air fry or bake as directed. This way, you can have delicious, homemade protein bagels ready with minimal effort, ensuring you start your day on a nourishing note!

Protein Bagels with Greek Yogurt Recipe FAQs
How do I know if my Greek yogurt is fresh enough to use in the bagels?
Absolutely! When selecting Greek yogurt, look for containers without any bloating or breaks in the seal. The yogurt should be creamy, not overly watery, and check the expiration date. If you see any green or dark spots or an off smell, it’s best to discard it. Fresh yogurt gives the best texture and flavor to your bagels.
What’s the best way to store leftover protein bagels?
For optimal freshness, place your protein bagels in an airtight container in the refrigerator. They’ll stay delicious for up to 3 days. You can also store them at room temperature for a day if you plan to eat them soon, but avoid longer storage to keep that delightful texture.
Can I freeze protein bagels, and if so, how?
Very! To freeze, wrap each cooled bagel tightly in plastic wrap, ensuring there are no exposed areas. Then, place the wrapped bagels in a freezer-safe zip-top bag. You can keep them frozen for up to 3 months. When you’re ready to enjoy, just toast them straight from the freezer; they’ll be wonderfully warm and satisfying!
What should I do if my bagel dough is too sticky?
No worries! If the dough feels overly sticky while mixing, you can sprinkle in more gluten-free flour, a tablespoon at a time, until it’s manageable. Alternatively, dust your hands and the working surface with flour while you shape the dough—this prevents it from sticking and keeps the bagels smooth and lovely!
Are these bagels suitable for someone with nut allergies?
Yes, these protein bagels are nut-free, as they primarily consist of gluten-free flour and Greek yogurt. However, always double-check any substitutes you might use, like specific seasonings or toppings, to ensure they align with your dietary needs. It’s super important to read labels for hidden allergens!
Can I customize the toppings for variety?
The more the merrier! You can absolutely experiment with various toppings for your protein bagels. Besides Everything But The Bagel seasoning, try sesame seeds, cinnamon sugar, or even a mix of cheese and herbs. Get creative and make them a perfect fit for your taste buds!

Protein Bagels Made Easy: Quick, Gluten-Free Delight!
Equipment
- Air fryer
Ingredients
For the Bagels
- 1 cup gluten-free all-purpose flour Substitute with all-purpose flour if gluten isn’t a concern.
- 1 tsp baking powder Essential for achieving that perfect bagel lift and texture.
- 1 pinch salt Enhances flavor and balances sweetness.
- 1 cup plain unsweetened Greek yogurt Can be replaced with cottage cheese blended until smooth.
For Topping
- Everything But The Bagel Seasoning Can also be switched with sesame seeds or your favorite spice mix.
Instructions
How to Make Protein Bagels
- In a large bowl, mix the gluten-free flour, baking powder, and pinch of salt until well combined.
- Stir in the Greek yogurt, blending until a cohesive dough forms.
- Divide the dough into two equal parts, then shape each into a smooth ball.
- Roll each ball into a rope, pinching the ends together to create the classic bagel shape.
- Set your air fryer to 350°F, letting it warm up for about 5 minutes.
- Lightly spray the bagels with non-stick spray or drizzle olive oil over them, then sprinkle your Everything But The Bagel Seasoning on top.
- Place the bagels in the air fryer and cook for about 8 minutes until golden brown, flipping and air frying for an additional 2-3 minutes for extra crispiness.
























