Wholesome Air Fryer High Protein Bagels: Gluten-Free & Fiber-Rich with Cottage Cheese & Oat Flour
Achieving your daily fiber and protein goals has never been more delightful or effortless than with this incredible recipe for our satisfying High Protein Bagels. Crafted with wholesome oat flour, these bagels offer a perfectly chewy texture, are made with simple ingredients, and boast a remarkably fast cook time thanks to the magic of the Air Fryer! Prepare to fall in love with a healthy breakfast option that doesn’t compromise on taste or convenience.

While TikTok popularized the concept of 3-ingredient bagels, incorporating oat flour takes this trend to a whole new level. This small change is a true game-changer, especially if you, like me, are looking to significantly increase your fiber intake. As someone who enjoys oatmeal frequently, the idea of transforming oats into a delicious bagel was incredibly exciting—and even more so when I discovered how wonderfully it works!
Through various tests, I experimented with both Greek yogurt and cottage cheese as the primary protein source. Both options yielded acceptable results, but I found myself particularly drawn to the exceptionally fluffy texture achieved with the cottage cheese batch. This discovery cemented cottage cheese as the star ingredient for these easy, protein-packed bagels.
These easy cottage cheese bagels make incorporating ample protein into your diet incredibly simple. I often transform them into a hearty breakfast sandwich, pairing them with fluffy eggs and savory turkey bacon, my flavorful homemade sausage patties, or a slice of lean ham. Beyond breakfast, they are fantastic toasted with a smear of cream cheese, a dollop of peanut butter, or even a generous scoop of this healthy chicken salad for a protein-rich snack that effectively curbs those pesky mid-day cravings.
When it comes to other outstanding protein-rich breakfast options, we are big fans of our Cheesy Bacon Breakfast Bites. In fact, if you made them slightly larger, they would make an absolutely perfect, savory filling for these very bagels, adding another layer of flavor and protein!
For an extra burst of flavor and texture, I love to crown this recipe with a sprinkle of our signature Homemade Everything Bagel Seasoning. It adds that classic bagel shop finish right in your own kitchen.
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More Reasons To Love These High Protein Bagels
Beyond being incredibly delicious and easy to make, these air fryer high protein bagels offer a multitude of benefits that make them a staple in any health-conscious kitchen:
- Naturally Gluten-Free & High in Fiber: This innovative recipe uses oat flour, providing a wonderful gluten-free alternative to traditional wheat-based bagels. Oat flour also significantly boosts the fiber content, which is essential for digestive health, blood sugar regulation, and prolonged satiety. It’s a fantastic way to enjoy a classic comfort food without the gluten!
- Remarkably Simple and Quick to Make: Don’t be intimidated by homemade bagels! This recipe is designed for ease and speed. Even beginner bakers will find success with minimal effort. The air fryer drastically cuts down on baking time, allowing you to whip up fresh, warm bagels in under 30 minutes—perfect for busy mornings or spontaneous snack attacks.
- Effectively Curbs Bagel Cravings (Healthier Version!): If you often crave the comforting chewiness of a bagel but want a healthier option, look no further. These homemade high-protein bagels deliver all the satisfaction of a store-bought bagel but with a superior nutritional profile. They’re packed with protein to keep you full and fiber to support your overall wellness, making them a smart choice over conventional, often carb-heavy, alternatives.
If you’re on the hunt for more fantastic gluten-free meal options that are both nutritious and delicious, be sure to explore our other favorites: our protein-packed Gluten Free Greek Yogurt Pizza Crust, our beloved Momma’s Gluten Free Meatloaf recipe, and these convenient Gluten Free Make Ahead Freezer Waffles!
Key Ingredients for Healthy Bagels
You’ll be delighted by how few ingredients are required to create these incredible high-protein bagels. Each component plays a vital role in achieving their perfect texture and flavor. For precise measurements and a complete list, please refer to the printable recipe card located further down.

- Gluten-Free Oat Flour: This is the foundation of our high-fiber bagels. I highly recommend Bob’s Red Mill brand for its consistent quality. Oat flour provides a naturally gluten-free base and adds a significant amount of dietary fiber, contributing to the bagels’ chewy yet tender crumb.
- Cottage Cheese: The secret to the high protein content and delightful fluffiness! Opt for a thick, good-quality brand like Good Culture, or you can substitute with plain Greek yogurt for a similar effect. Ensure you strain out any excess liquid from the cottage cheese to prevent a sticky dough. (Both options are pictured above, but remember to use only one!)
- Baking Powder: This leavening agent is crucial for giving the bagels their characteristic puff and light texture in the air fryer.
- Salt: A pinch of salt enhances all the other flavors, balancing the mildness of the oat flour and cottage cheese.
- Garlic Powder: Adds a subtle savory depth, making these bagels incredibly versatile for various toppings and fillings.
- Egg or Liquid Egg Whites: Used to create a shiny, golden-brown egg wash, which also helps the toppings adhere to the bagels during cooking.
Creative Variations & Favorite Bagel Toppings
One of the best things about these homemade protein bagels is their incredible versatility! You can easily customize them to suit your cravings, whether you prefer sweet or savory profiles. Here are some fantastic ideas to get you started:
- Classic Savory: As seen in the photos, sesame seeds and our Homemade Everything Bagel Seasoning are timeless favorites that add a fantastic crunch and aromatic flavor.
- Sweet Indulgence: For a sweeter take, mix some cinnamon and raisins into the dough, or sprinkle them on top before baking. A light dusting of brown sugar with cinnamon also works beautifully.
- Spicy & Cheesy: If you love a kick, try adding finely diced jalapeños and shredded cheddar cheese to the dough or as a topping. The cheese will melt beautifully, creating a savory, spicy treat.
- More Topping Ideas to Experiment With:
- Poppy Seeds: For a classic bagel shop look and a delicate nutty flavor.
- Flaky Sea Salt: A simple yet effective way to add a burst of savory goodness.
- Chocolate Chips: For a delightful dessert-style bagel (mini chips work best!).
- Blueberries: Fresh or frozen (not thawed) blueberries can be folded into the dough for a fruity twist.
- Feel free to get creative and mix and match your favorite flavors! The possibilities are endless.
Step by Step Air Fryer Bagel Instructions
Creating these delicious high-protein bagels in your air fryer is a straightforward process. Follow these simple steps for perfectly golden and chewy results. For a detailed, printable version, please see the recipe card below.

Step 1: Combine Dry and Wet Ingredients. In a large mixing bowl, start by adding all your dry ingredients: the gluten-free oat flour, salt, garlic powder, and baking powder. Whisk them together thoroughly until well combined. Next, add the strained cottage cheese. Using a fork or spatula, mix the ingredients until they are fully incorporated. The mixture will initially have a crumbly, coarse texture, which is exactly what you want.

Step 2: Knead the Dough. Transfer the crumbly mixture to a lightly floured surface or continue kneading directly in the bowl. Knead the dough vigorously for about 2 minutes. As you knead, it will gradually come together, becoming smooth and tacky to the touch, but not overly sticky. If the dough feels too sticky to handle, add an additional tablespoon of oat flour at a time until the desired consistency is achieved. Avoid adding too much flour, as this can make the bagels dry.

Step 3: Shape Your Bagels. Divide the prepared dough into four equal portions. There are two primary ways to shape your bagels:
- Rope Method: Roll each dough portion into a rope approximately 3/4-inch thick. Bring the ends of the rope together and firmly pinch them to form a classic bagel shape.
- Poke-Hole Method: Alternatively, you can roll each portion into a smooth ball. Then, gently poke a hole in the center of each ball using your finger. Carefully stretch out the hole to enlarge it slightly, as the bagels will puff up during cooking.

Step 4: Egg Wash and Season. In a small bowl, lightly beat one egg to create an egg wash. Using a pastry brush, gently coat both sides of each shaped bagel with a light layer of the egg wash. This will help them achieve a beautiful golden crust and ensure your chosen seasonings adhere properly. Generously sprinkle your preferred seasoning on both sides. As pictured, a mix of everything bagel seasoning and sesame seeds works wonderfully.

Step 5: Air Fry to Golden Perfection. Begin by preheating your air fryer to 350°F (175°C) for 5 minutes. While it’s preheating, lightly spray the air fryer basket with nonstick cooking spray to prevent sticking. Carefully place the seasoned bagels into the preheated air fryer basket, ensuring they are not overcrowded. Air fry for approximately 15 minutes, or until the bagels turn a beautiful golden brown and are cooked through. Cooking times may vary slightly depending on your air fryer model.

Step 6: Cool, Slice, and Enjoy! Once air-fried, carefully remove the bagels from the basket and place them on a wire rack to cool for at least 10 minutes. This cooling period is important as it allows the bagels to set and prevents them from becoming gummy when sliced. After cooling, slice them in half, add your favorite toppings, and savor your homemade, high-protein, fiber-packed bagels!
Helpful Tips for Perfect High Protein Bagels
To ensure your high-protein bagels turn out perfectly every time, keep these expert tips in mind:
- Strain Your Cottage Cheese: While there’s no need to blend the cottage cheese for this recipe (the curds add a nice texture!), it is absolutely essential to strain out any extra liquid. Excess moisture will make your dough excessively sticky and difficult to work with, affecting the final texture of your bagels. A fine-mesh sieve or cheesecloth works best.
- Flour Your Hands and Work Surface: The dough for these bagels can be a bit tacky. To prevent it from sticking to your hands and your countertop during kneading and shaping, make sure to lightly flour both. This creates a barrier, making the dough much more manageable.
- Enlarge the Center Hole: When shaping your bagels, create the center hole slightly larger than you think necessary. This is because the dough will puff up during the air frying process, causing the hole to shrink a little. A larger initial hole ensures you have a distinct bagel shape after cooking.
- Flour Substitutions (Use with Caution):
- Do NOT Substitute Almond Flour or Coconut Flour: These flours have vastly different absorption rates and gluten structures, and have not been tested with this recipe. They will likely not yield the desired chewy, bagel-like texture.
- Gluten-Free 1:1 Flour or All-Purpose Self-Rising Flour: If oat flour is unavailable or if you prefer a fluffier (though less fibrous) bagel, you can substitute with a gluten-free 1:1 baking flour blend or an all-purpose self-rising flour. Adjust liquid content as needed, as absorption rates may vary.
- Whole Wheat Flour (if not gluten-free): If you don’t require the bagels to be gluten-free, whole wheat flour can be a good substitute, offering a similar fiber boost and hearty texture.
- Adjusting for Larger Bagels: This recipe yields four standard-sized mini bagels. If you prefer bigger bagels, simply increase both the oat flour and cottage cheese, ensuring you maintain a 1:1 ratio. I’ve successfully made larger batches using 1 1/3 cups of each ingredient, or even up to 2 cups of each for a truly substantial bagel.
Meal Prep and Storage Tips
These high-protein bagels are not only delicious fresh but also fantastic for meal prepping, ensuring you have a healthy and convenient breakfast or snack ready throughout the week.
Prep Ahead: This recipe is a fantastic candidate for meal prepping. Make a batch or two on the weekend, and you’ll have easy, protein-packed breakfast sandwiches or quick snacks at your fingertips for the entire week!
To Store: Once cooled completely, store your gluten-free bagels in an airtight container in the refrigerator. They will maintain their freshness and quality for up to 3 days. For longer storage, these bagels freeze exceptionally well. We highly recommend vacuum sealing them for the best results and to prevent freezer burn.
To Reheat: When you’re ready to enjoy a stored bagel, reheating is simple. Slice your bagel in half and toast it in a toaster oven using the bagel setting if available, for a perfectly crispy exterior and warm interior. Alternatively, you can reheat them in your air fryer for a couple of minutes at 300°F (150°C) until warmed through and lightly crisped.

Frequently Asked Questions (FAQs)
Absolutely! Making your own oat flour is incredibly easy and cost-effective. Simply take old-fashioned or rolled oats and blend them in a high-speed blender or food processor until a fine, powdery flour forms. Ensure there are no large oat pieces left for the best dough consistency.
This recipe is specifically designed to boost protein content in bagels by incorporating cottage cheese directly into the dough. Cottage cheese is a fantastic, versatile source of extra protein that also contributes to a delightful texture. For an even greater protein boost, consider topping your bagel with protein-rich spreads like Greek yogurt cream cheese, nut butter, or using it as a base for a breakfast sandwich with eggs and lean meats.
Each of our delicious high-protein bagels contains an impressive 13 grams of protein. This makes them an excellent choice for a satisfying breakfast or snack that helps keep you feeling full and supports your daily protein needs.
I have not tested this recipe with almond flour or coconut flour, and I generally would not recommend them as direct substitutions. These flours behave very differently from oat flour in terms of liquid absorption and binding properties, and they are unlikely to yield the desired bagel texture. For best results, stick with oat flour. If you don’t have oat flour, a gluten-free 1:1 all-purpose flour blend or a self-rising flour could work, but be aware the fiber content might be lower.
Yes, absolutely! If you don’t own an air fryer or wish to bake a larger batch simultaneously, you can easily adapt this recipe for a conventional oven. Simply bake the shaped bagels at 375°F (190°C) until they are puffed up and beautifully golden brown. This typically takes approximately 25-30 minutes, though cooking times may vary by oven.

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Air Fryer GF Protein Bagels (High Fiber)
Nancylynn
4 bagels
Pin Recipe
10 minutes
15 minutes
25 minutes
Equipment
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Air Fryer
Ingredients
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1 Cup Gluten Free Oat Flour + more for kneading and to add if dough feels too sticky -
1 Cup Cottage Cheese extra liquid strained out – I like a thick brand like Good Culture; or sub plain Greek yogurt -
2 tsp Baking Powder -
Pinch salt and garlic powder -
1 Egg beaten for egg wash -
Sesame Seeds optional for topping -
Everything Bagel Seasoning optional for topping
Instructions
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In a medium sized bowl, combine the flour, salt, garlic powder, and baking powder and whisk well. Add the strained cottage cheese and mix with a fork or spatula until well combined, it will look like small crumbles.
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Using your clean hands, working in the bowl, knead the dough until it comes together and is smooth, tacky, but not sticky, about 2 minutes. If you need to add more flour, do so 1 Tablespoon at a time.
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Divide dough into 4 equal balls. Roll each ball into 3/4-inch thick ropes and join the ends to form bagels. Or you can make a ball and poke a hole in the center, then stretch it slightly.
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Top with egg wash and sprinkle both sides with seasoning of your choice.
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Preheat the air fryer to 350 for 5 minutes. Spray the air fryer basket with nonstick spray and air fry for 15 minutes, until golden brown.
Notes
WW: 4 points (per bagel) [Calculated using low fat cottage cheese]
For detailed helpful tips on making perfect bagels, please refer to our comprehensive “Helpful Tips for Perfect High Protein Bagels” section above. It covers everything from dough consistency to flour substitutions!
Oven Instructions: If you prefer to bake these bagels in a conventional oven, preheat your oven to 375°F (190°C). Bake the bagels until they are puffed and golden brown, which typically takes about 25-30 minutes.
Prep Ahead: This recipe is great for meal-prep. Make these amazing bagels and have easy breakfast sandwiches for the week!
To Store: Store your gluten-free bagels in an airtight container in the fridge. They will keep for 3 days. They can be kept for longer in the freezer. We recommend vacuum sealing for the best results.
To Reheat: Reheat your sliced bagels in the toaster using the bagel setting, if available. You can also reheat in the airfryer for a couple of minutes.
Nutrition
Calories: 179kcal
Carbohydrates: 22g
Protein: 13g
Fat: 4g
Saturated Fat: 1g
Polyunsaturated Fat: 1g
Monounsaturated Fat: 1g
Trans Fat: 0.01g
Cholesterol: 43mg
Sodium: 463mg
Potassium: 175mg
Fiber: 4g
Sugar: 2g
Vitamin A: 83IU
Calcium: 175mg
Iron: 2mg
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