Gluten-Free Protein Bagel Bites

Enjoy this twist on a childhood favorite — Gluten-Free Protein Bagel Bites!

There’s plenty of protein in both the dough for these bagel bites (yes, homemade bagels!), as well as the toppings. The dough is made with cottage cheese and gluten-free flour, which gives the bagel bites their body and delivers a healthy source of protein. Rather than boiling the bagels, you’ll shape them and bake them until they become golden brown and crispy. Not only do they look great, but it’s a mess-free, hands-off method.

Top each bagel bite with your favorite pizza toppings. I like to smear them with pizza sauce, shredded mozzarella, Parmesan cheese, pepperoni, and salami. Feel free to customize them based on your flavor and dietary preferences. They’re a slightly healthier take on the microwave classic that is sure to please kids and adults alike!

ingredients:

• Whole Milk Cottage Cheese (See Note)
• Freshly Squeezed Lemon Juice
• Baking Powder
• Kosher Salt
• Dried Oregano
• Gluten-Free Flour
• Large Egg
• Flaky Salt
• Pizza Sauce
• Shredded Mozzarella
• Pepperoni Slices
• Genoa Salami
• Freshly Grated Parmesan Cheese
• Chili Flakes

step by step:

step one: prep the oven

Preheat the oven to 375°F. Line a baking sheet with parchment paper and set aside.

step two: make the bagel dough

In a wide-mouth jar or quart-sized container, add the cottage cheese, lemon juice, baking powder, salt, and dried oregano. Use an immersion blender to blend until the mixture is completely smooth. Transfer the mixture to a medium mixing bowl. Add 1 cup of flour to the cottage cheese mixture. Using a wooden spoon, stir together until a shaggy dough forms. It will be quite sticky at this point.

step three: knead the dough

Lightly dust a cutting board with the remaining 1 tablespoon of flour and spread to coat the surface. Turn the dough onto the floured board. Begin kneading the dough, adding flour if it becomes too sticky, until a dough ball forms. Using a knife or bench scraper, divide the dough into 8 even pieces.

step four: shape the dough

Using clean hands, roll all 8 portions into individual balls. Transfer to the baking sheet, leaving about 2 inches between each. Gently pat them down to flatten a bit. Using the end of a wooden spoon or your pointer finger, press down in the center of each ball to make a hole. Stretch the dough a bit to smooth out the inside, making a mini bagel! Don’t fret if the hole disappears a bit while baking.

step five: bake the bagels

Brush the tops of each bagel with egg wash and top with flaky salt. Transfer to the oven and bake for 15 minutes on the middle rack. After 15 minutes, transfer to the upper rack and bake for another 10 minutes until the bagels are crisp on the exterior and golden brown on the outside. When tapped, they should sound a bit hollow. If they feel too soft, bake for an additional 5 minutes at 350°F. Allow to cool completely before cutting in half with a serrated knife. If you cut them while warm, they will be gummy.

step six: add your toppings

Increase the oven temperature to 400°F. Top each bagel with a few teaspoons of sauce, spreading to the edges. Add the mozzarella, pepperoni, sausage, and Parmesan cheese. Bake for 10 minutes or until the cheese is melted. For an extra bubbly top, broil for 1 to 2 minutes.

step seven: garnish and serve

Garnish with chili flakes, if desired. Allow to cool slightly before serving.

recipe faqs:

I hope y’all love these Gluten-Free Protein Bagel Bites as much as my family does! Comment below and let me know what you think!

looking for more gluten-free recipes? try these!

Skillet Pizza Penne

Grilled Chipotle Steak Nachos

One-Pot Gluten-Free Mac and Cheese

5 from 4 votes

Gluten-Free Protein Bagel Bites

Prep: 25 minutes mins

Cook: 40 minutes mins

Total: 1 hour hr 5 minutes mins

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Ingredients 

For the Bagel:

• ▢ 1 cup whole milk cottage cheese (see note)
• ▢ 2 teaspoons freshly squeezed lemon juice
• ▢ 1½ teaspoons baking powder
• ▢ 1/2 teaspoon kosher salt
• ▢ 1 teaspoon dried oregano
• ▢ 1 cup plus 1 tablespoon gluten-free flour, divided
• ▢ 1 large egg, beaten
• ▢ flaky salt, to garnish

For the Toppings:

• ▢ 6-8 tablespoons pizza sauce
• ▢ 1 cup shredded mozzarella cheese
• ▢ 16 pepperoni slices, diced small
• ▢ 4 slices Genoa salami diced small
• ▢ 1/4 cup freshly grated Parmesan cheese
• ▢ chili flakes, optional

Instructions 

• Preheat the oven to 375°F. Line a baking sheet with parchment paper and set aside.
• In a wide-mouth jar or quart-sized container, add the cottage cheese, lemon juice, baking powder, salt, and dried oregano. Use an immersion blender to blend until the mixture is completely smooth. Transfer the mixture to a medium mixing bowl. Add 1 cup of flour to the cottage cheese mixture. Using a wooden spoon, stir together until a shaggy dough forms. It will be quite sticky at this point.
• Lightly dust a cutting board with the remaining 1 tablespoon of flour and spread to coat the surface. Turn the dough onto the floured board. Begin kneading the dough, adding flour if it becomes too sticky, until a dough ball forms. Using a knife or bench scraper, divide the dough into 8 even pieces.
• Using clean hands, roll all 8 portions into individual balls. Transfer to the baking sheet, leaving about 2 inches between each. Gently pat them down to flatten a bit. Using the end of a wooden spoon or your pointer finger, press down in the center of each ball to make a hole. Stretch the dough a bit to smooth out the inside, making a mini bagel! Don’t fret if the hole disappears a bit while baking.
• Brush the tops of each bagel with egg wash and top with flaky salt. Transfer to the oven and bake for 15 minutes on the middle rack. After 15 minutes, transfer to the upper rack and bake for another 10 minutes until the bagels are crisp on the exterior and golden brown on the outside. When tapped, they should sound a bit hollow. If they feel too soft, bake for an additional 5 minutes at 350°F. Allow to cool completely before cutting in half with a serrated knife. If you cut them while warm, they will be gummy.
• Increase the oven temperature to 400°F. Top each bagel with a few teaspoons of sauce, spreading to the edges. Add the mozzarella, pepperoni, sausage, and Parmesan cheese. Bake for 10 minutes or until the cheese is melted. For an extra bubbly top, broil for 1 to 2 minutes.
• Garnish with chili flakes, if desired. Allow to cool slightly before serving.

Notes

Cottage cheese really varies in texture. This recipe has been tested with three kinds of cottage cheese, all with varied results. For the best results, I suggest using a thicker cottage cheese, such as Good Culture. If you can’t find Good Culture, look for “small curd” cottage cheese, which means it is a little less watery. If your dough is not coming together into a disk and is too sticky, add flour in 1 tablespoon increments until you’ve reached the right consistency.

Nutrition

Calories: 1443kcal, Carbohydrates: 107g, Protein: 90g, Fat: 76g, Saturated Fat: 34g, Polyunsaturated Fat: 6g, Monounsaturated Fat: 26g, Trans Fat: 1g, Cholesterol: 364mg, Sodium: 5372mg, Potassium: 919mg, Fiber: 15g, Sugar: 15g, Vitamin A: 1910IU, Vitamin C: 12mg, Calcium: 1552mg, Iron: 9mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Author: Alex Snodgrass

Calories: 1443

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