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30 Minutes or Less

5-Ingredient Cottage Cheese Pizza Bagels (high-protein & gluten-free!)

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close up image of cottage cheese pizza bagels on a baking sheet.

There’s just something about a pizza bagel that takes me straight back to the year 2003. Fun fact: pizza bagels were the first thing I learned how to “cook.” The frozen ones, of course. My mom showed me how to pop them in the toaster oven, what setting to cook them on, and in just a few minuets I had the most delicious little lunch! These cottage cheese pizza bagels are just as good as I remember the frozen ones being – just a grown-up, higher-protein, & gluten-free version! A simple three-ingredient bagel dough made from blended cottage cheese and flour is baked until golden, then sliced open, topped with pizza sauce, melty cheese, and pepperoni, and broiled until bubbly.

What I love most about this recipe is how insanely simple the bagel dough is. No yeast, no boiling, no rising time, no kneading machine – just cottage cheese, flour, and baking powder mixed into a dough and baked. The cottage cheese melts completely into the dough as it bakes, adding protein and moisture without any detectable cottage cheese flavor. If you’re already a fan of my Cottage Cheese Pizza Crust or Cottage Cheese Wrap, these pizza bagels are going straight to the top of your list!

pulling apart a cottage cheese pizza bagel.

Why You’ll Love These Cottage Cheese Pizza Bagels

  • Just 5 ingredients – and they taste like the real thing. Cottage cheese bagel dough topped with pizza sauce, shredded cheese, and pepperoni. That’s the whole recipe, and it genuinely tastes like the pizza bagels you grew up on, with a serious protein upgrade.
  • Higher in protein than regular bagels. Thanks to the cottage cheese in the dough, these bagels have significantly more protein than anything you’d find at a bakery or grab from a box. It’s an easy, sneaky protein boost that nobody will ever taste.
  • Easily made gluten-free. Simply swap the all-purpose flour for a gluten-free all-purpose flour blend and you’ve got a completely gluten-free pizza bagel that nobody will know the difference on. I used gluten-free all-purpose flour and they came out perfect!

Sam’s Recipe Tips

  • Start with 1½ cups of cottage cheese, then add more if needed. The amount of cottage cheese you need can vary depending on the brand, fat percentage, and how much liquid it contains. Start with 1½ cups, mix it into the flour, and check the dough consistency. If it’s too dry or crumbly, add more cottage cheese a tablespoon at a time until it comes together into a smooth, workable dough.
  • Don’t skip the cooling time after baking. I know it’s tempting to slice right into the fresh-baked bagels, but letting them cool for at least 20 minutes is essential. The interior needs that time to fully set, slicing too early results in a gummy, doughy center that doesn’t hold up to toppings. Trust the process!
  • Watch the broiler closely. The pizza bagels go from perfectly bubbly to burnt very quickly under the broiler. Stay close to the oven and check every 30 seconds after the first minute. The moment the cheese is melted and starting to bubble and brown, pull them out!
  • Make the bagels ahead. The plain baked bagels (before the pizza topping) store beautifully in an airtight container at room temperature for up to 2 days, or in the freezer for up to 1 month. Toast from frozen, add your toppings, and broil – fresh pizza bagels in minutes!
overhead image of cottage cheese pizza bagels on a baking sheet.

Flavor Variations & Topping Options

The pizza bagel is just the beginning – this cottage cheese bagel dough is endlessly versatile!

🧅 Everything Bagel Before baking, brush the bagels with egg wash and sprinkle generously with everything bagel seasoning. Serve with cream cheese or smoked salmon and capers – a classic!

🧄 Garlic Parmesan Brush the baked bagels with garlic butter (melted butter + garlic powder + a pinch of salt) and sprinkle with freshly grated parmesan. Broil for 1–2 minutes until golden and fragrant.

🫙 White Pizza Swap the pizza sauce for a creamy white sauce (ricotta, olive oil, and garlic), then top with mozzarella, fresh spinach, and a sprinkle of red pepper flakes. Broil until bubbly.

🍕 BBQ Chicken Spread BBQ sauce instead of pizza sauce, then top with shredded rotisserie chicken, mozzarella, and thinly sliced red onion.

🌶️ Spicy Arrabbiata Use a spicy arrabbiata sauce instead of regular pizza sauce, top with mozzarella and Italian sausage crumbles, and finish with fresh basil after broiling.

Sweet Variations:

  • Cinnamon Sugar – Mix cinnamon and sugar and sprinkle over the baked bagels while still warm, then drizzle with a simple glaze.
  • Blueberry & Cream Cheese – Spread with cream cheese and top with fresh blueberries and a drizzle of honey for a sweet bagel option.

Made this recipe? I’d love to see it! Tag me on Instagram @samdoesherbest or TikTok @samdoesherbest – I repost my favorites! And if you loved it, please leave a ⭐⭐⭐⭐⭐ rating and written review below. It means the world and helps other readers find this recipe!

close up image of cottage cheese pizza bagels on a baking sheet.
5 from 1 vote

5-Ingredient Cottage Cheese Pizza Bagels

These cottage cheese pizza bagels are a high-protein, easily gluten-free twist on the classic childhood favorite! Made with a simple three-ingredient cottage cheese bagel dough, topped with pizza sauce, melty cheese, and pepperoni, then broiled until perfectly bubbly. No yeast, no boiling, no complicated steps – just blend, mix, bake, and top for a fun, satisfying lunch or snack that comes together in under 30 minutes!
Print Pin Rate
Prep Time: 10 minutes
Cook Time: 15 minutes
Total Time: 25 minutes
Servings: 6 bagels

Equipment

  • 1 food processor or high speed blender
  • 1 medium bowl
  • 1 baking sheet

Ingredients

For the bagels:

  • 2 cups all-purpose flour I used gluten-free all purpose flour
  • 2 teaspoons baking powder
  • 1 1/2 – 2 cups cottage cheese

For the pizza topping:

  • 1/2 cup pizza sauce
  • 1 cup shredded Italian cheese blend or mozzarella
  • pepperoni optional

Instructions

  • Preheat oven to 400°F and line a baking sheet with parchment paper.
  • Blend cottage cheese until completely smooth.
  • Mix flour and baking powder together, then add blended cottage cheese and mix until a dough forms. Add more cottage cheese if the dough is too dry.
  • Divide dough into 6 balls, poke holes through each, and shape into bagels. Place on prepared baking sheet.
  • Bake for 20–22 minutes until golden brown. Cool for at least 20 minutes.
  • Slice each bagel open and place cut-side up. Spread pizza sauce on each half, top with cheese and pepperoni.
  • Broil for 1–3 minutes until cheese is melted and bubbly. Enjoy!

Notes

Nutritional info is for one whole bagel with toppings.
  • Start with 1½ cups cottage cheese and add more if the dough is too dry.
  • Let the bagels cool at least 20 minutes before slicing — this prevents a gummy interior.
  • Watch the broiler closely — the cheese can go from bubbly to burnt quickly!
  • Store plain baked bagels in an airtight container for up to 2 days, or freeze for up to 1 month.
  • For gluten-free, use a 1:1 GF flour blend. Avoid almond or coconut flour.

Nutrition

Serving: 1bagel | Calories: 195kcal | Carbohydrates: 24g | Protein: 11g | Fat: 6g | Fiber: 1g
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30 Minutes or Less

3-Ingredient Gluten-Free Bagel Bites

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Close up image of a gluten-free bagel bite with everything bagel seasoning and cream cheese.

I’ve been on a mission lately to switch up my breakfast recipes! I love a protein smoothie, and my 3 ingredient protein pancakes, but what I’ve really been craving is a bagel. But if you’re gluten-free like me, then you know how hard it can be to find a good gluten-free bagel. They’re all either too dense, hard, or just totally wrong and taste nothing like a bagel. But not these gluten-free bagel bites! They’re nice and toasted on the outside, but perfectly soft and fluffy on the inside. I love topping mine with a little everything bagel seasoning for extra flavor, but you can add whatever toppings or mix-ins you’d like! These 3 ingredient bagel bites are also one of the easiest gluten-free recipes you’ll ever make. Thank me later!

Why You’ll Love This Recipe

  • Super Simple & Quick – Made with just three ingredients, these bagel bites are ready in under 30 minutes.
  • Gluten-Free & Healthier – A great alternative to store-bought bagel bites with no preservatives or additives.
  • Customizable & Versatile – Top with everything bagel seasoning, cheese, or even cinnamon sugar for a sweet twist.
Close up image of gluten-free bagel bites with everything bagel seasoning on a plate with cream cheese on the side.

What You’ll Need to Make Gluten-Free Bagel Bites

Gluten-Free All-Purpose Flour – Provides the perfect structure and texture while keeping this recipe gluten-free. I use and love Bob’s Red Mill Gluten-Free 1 to 1 Baking Flour in many of my gluten-free recipes. Though for extra fluffy bagel bites, I recommend using King Arthur’s Gluten-Free Bread Flour instead.

Baking Powder – Helps the bagel bites rise and stay fluffy inside.

Plain Greek Yogurt – Adds moisture, binds the dough, and gives the bagels a slightly tangy flavor, similar to traditional bagels.

How to Make Gluten-Free Bagel Bites

  1. Preheat & Prepare – Set the oven or air fryer to 350°F and line a baking sheet with parchment paper.
  2. Mix the Dough – In a bowl, combine the flour and baking powder. Stir in the Greek yogurt until a dough forms. If the mixture is too dry, add a little more yogurt.
  3. Shape the Bagel Bites – Roll about 2 tablespoons of dough into small balls and place them on the baking sheet.
  4. Add Toppings – Brush with egg wash (optional) and sprinkle with everything bagel seasoning.
  5. Bake or Air Fry – Bake for 15-20 minutes (or air fry for 12-15 minutes) until golden brown.
  6. Serve & Enjoy – Let cool slightly and enjoy warm with butter or cream cheese.
A gluten-free bagel bite with a bite taken out of it.

Topping Options

  • Savory: Everything bagel seasoning, sesame seeds, poppy seeds, shredded cheese
  • Sweet: Cinnamon sugar, honey drizzle, chocolate chips

Adjust This Recipe to Your Dietary Needs

  • Make it Dairy-Free: Use dairy-free Greek style yogurt to make the dough.
  • Make it Vegan: Use plant-based yogurt and skip the egg wash!
  • Make it Keto: Swap the gluten-free all purpose flour for almond flour.
Close up image of a gluten-free bagel bite with everything bagel seasoning and cream cheese.
5 from 1 vote

Gluten-Free Bagel Bites

These 3-ingredient gluten-free bagel bites are soft, chewy, and perfect for breakfast, snacks, or on-the-go meals. Made with simple pantry staples, they come together in minutes and can be baked or air-fried for a quick, satisfying treat.
Print Pin Rate
Prep Time: 5 minutes
Cook Time: 15 minutes
Total Time: 20 minutes
Servings: 10 bagel bites

Equipment

  • 1 large bowl

Ingredients

  • 1 cup gluten-free all purpose flour
  • 1 teaspoon baking powder
  • 1 cup plain Greek yogurt

For topping:

  • 1 egg whisked
  • 2 tablespoons everything bagel seasoning

Instructions

  • Preheat oven to 350° Fahrenheit and line a baking sheet with parchment paper. Or, preheat your air fryer to 350° Fahrenheit.
  • Mix together the gluten-free all purpose flour and baking powder in a large bowl. Then, add in the plain Greek yogurt and mix until a dough comes together (you may need to use your hands to help bring the dough together). If the dough seems dry and won’t come together in a ball, try adding an additional 1-3 tablespoons of Greek yogurt to the dough.
  • Scoop about 2 tablespoons of dough and roll it between the palms of your hands to form a ball. Place each ball on your prepared baking sheet or inside the basket of your preheated air fryer. Lightly brush the top of each bagel bite with the egg wash, then sprinkle with everything bagel seasoning.
  • Bake the gluten-free bagel bites for 15-20minutes, or until lightly golden. Or, if you’re using an air fryer, air fry the bagel bites at 350° Fahrenheit for 12-15 minutes. Remove the bites from the oven or air fryer and let cool slightly before serving warm with butter and cream cheese.

Nutrition

Serving: 1bagel bite | Calories: 50kcal | Carbohydrates: 9g | Protein: 3.5g | Sugar: 1.5g
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30 Minutes or Less

Magic 3-Ingredient Gluten-Free Bagels

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These 3-ingredient gluten-free bagels are truly magic! No yeast, kneading, rising, or boiling in water required. Just three simple ingredients, and these bagels are ready to eat in 30 minutes!

gluten-free bagels on a baking sheet with cream cheese on the side.

I like to think I know a thing or two about bagels. Not only were they my favorite food growing up, but I currently live in Brooklyn – home of the BEST BAGELS in the WORLD! So ya, I’ve had some really good bagels. A bagel should be toasty on the outside, fluffy on the inside, easy to slice through, and ready for toasting – and these gluten-free bagels are just that.

Now I’m sure you’re wondering – Sam, why bother making your own bagels if you can just buy literally the world’s best bagels from that place down the street. Well, I’ll tell you exactly why – because I can’t find a single good gluten-free bagel! They’re near impossible to track down. And the ones I do find are either too dense or extremely overpriced (or both). So I quickly realized if I wanted a gluten-free bagel, I’d just have to make it myself. And that, friends, is how the magic 3-ingredient gluten-free bagel was born!

3 gluten-free bagels stacked on top of each other.

What You’ll Need to Make 3-Ingredient Gluten-Free Bagels

Gluten-Free All Purpose Flour – Your gluten-free flour must contain xanthan gum! If it doesn’t, add 1/2 teaspoon of xanthan gum to this recipe. Gluten-free all purpose flours I use and recommend are Bob’s Red Mill Gluten-Free Baking Flour and King Arthur Gluten-Free Flour, both of which contain xanthan gum. I used the King Arthur flour in these bagels and they turned out perfect!

Baking Powder – We replace the yeast found in traditional bagel recipes with baking powder. Baking powder makes it so we don’t have to wait for our bagel dough to rise before baking. Instead, we can simply shape, then bake these bagels right away – super easy!

Greek Yogurt – Any plain and unsweetened Greek yogurt will work in this gluten-free bagels recipe! I even used Kite Hill’s non-dairy Greek yogurt to make my bagels dairy-free.

gluten-free bagels on a plate with cream cheese on the side.

Adjust This Recipe to Your Dietary Needs

Make it Vegan: To make vegan and gluten-free bagels, use a vegan greek yogurt and leave off the egg wash.

gluten-free bagels on a baking sheet with cream cheese on the side.
4.07 from 80 votes

Magic 3-Ingredient Gluten-Free Bagels

These 3-ingredient gluten-free bagels are truly magic! No yeast, kneading, rising, or boiling in water required. Just three simple ingredients, and these bagels are ready to eat in 30 minutes!
Print Pin Rate
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Servings: 6 bagels

Ingredients

  • 2 cups gluten-free all purpose flour, see Noted
  • 2 teaspoons baking powder
  • pinch of salt
  • 1-2 cups plain unsweetened Greek yogurt, dairy-free if necessary

For topping:

  • 1 large egg
  • 1 teaspoon water
  • pinch of salt
  • everything bagel seasoning, sesame seeds, poppy seeds, etc.

Instructions

  • Preheat oven to 400° Fahrenheit and line a baking sheet with parchment paper.
  • In a large bowl, whisk together the gluten-free all purpose flour, baking powder, and salt. Then, add in 1 cup of Greek yogurt and stir until a shaggy dough forms.
  • Using your hands, mix and form the dough into a smooth ball. If the dough seems too dry and won’t come together in a ball, add in more Greek yogurt – you may have to use an additional 1 cup of yogurt to reach the desired consistency.
  • Divide dough into 6 equal parts and shape each part into a ball. Use your thumbs to make a hole in the center of each ball, then gently pull to form a ring resembling a bagel.
  • Transfer bagels to the prepared baking sheet. Make the egg wash by whisking together the egg, water, and salt in a small bowl. Brush each bagel with egg wash and top with whatever toppings you’d like (or leave plain).
  • Bake bagels for 20-22 minutes, rotating baking sheet halfway through baking, until bagels are uniformly golden brown. Let cool slightly before slicing, topping, and eating.

Notes

  • Gluten-Free All Purpose Flour: Your gluten-free flour must contain xanthan gum, if it doesn’t add 1/2 teaspoon of xanthan gum to this recipe.
  • Gluten-free bagels will stay fresh in an airtight container in the fridge for up to 3 days. Or, you can freeze them for up to 3 months! Because of the yogurt, these do not keep well at room temperature.

    • Nutrition

    Calories: 300kcal
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