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May 2, 2025(updated October 23, 2025)

Baked Protein Bagels with Cottage Cheese (12g!)

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Are you looking for an easy-to-make, healthy homemade bagel recipe packed with protein? These oven-baked protein bagels with cottage cheese are the answer. Using just four main ingredients: flour, cottage cheese, and baking powder, these high-protein (12g!), no-boil bagels are light, fluffy, and delicious. Say hello to your new favorite high-protein breakfast (or lunch!).

Baked protein bagels with cottage cheese on a cooling rack.

Creamy, dreamy cottage cheese is a magical ingredient that can bump up the protein in your favorite healthy breakfast recipes. When I want a sweet breakfast, I use it to make high-protein pancakes. When I want a savory breakfast, I add it to a veggie-packed egg bake—and now I can’t stop using it to make these high-protein baked bagels!

They are addictively delicious—crispy on the outside and light and fluffy on the inside. Top them with everything but the bagel seasoning for a big boost of flavor. And then load them with your favorite bagel fillings.

💪 Looking for an extra protein boost? (This is the story of my life, lol!). Enjoy your cottage cheese bagels served with:

tuna salad
egg salad
chicken salad
Or use it as the base for your favorite breakfast sandwich.

So many delicious meals to eat, so little time, lol!

Let’s talk about the ingredients you’ll need

Don’t blink or you’ll miss the simplicity of this recipe. All you need are these five everyday ingredients (so easy peasy!).

An egg near bowls of cottage cheese, flour, baking powder and seasoning.

Flour: Unbleached all-purpose flour serves as the base of the dough, providing the bagels with structure while maintaining their soft and chewy texture. I tested this recipe with whole wheat flour and oat flour as well. While they both work, they yield a denser end product.
Baking powder: Don’t skip this (trust me, I learned the hard way 😂). It helps the bagels rise without yeast.
Cottage cheese: The star of the show! I always use the low-fat variety and love the taste and texture of Good Culture cottage cheese. It’s so good.
Egg: While an egg wash isn’t required, I highly recommend it. Brushing a little beaten egg over the bagels before baking gives them that gorgeous golden-brown color and helps the toppings stick. When I tested the recipe without it, the bagels still tasted great—but they looked a little pale and didn’t have that classic, glossy bakery finish. So if you’re not avoiding eggs, it’s a small extra step that makes a big difference.
Optional toppings: Customize your bagels with everything bagel seasoning, seeds, dried aromatics, or shredded cheese for extra crunch and flavor.

Can I Make Gluten-Free Cottage Cheese Bagels?

Yes! When I made this recipe, I tested a couple of different options because I know some of our readers follow a gluten-free diet. Here’s what I discovered:

1. You can easily substitute the all-purpose flour with an all-purpose gluten-free flour. Look for a blend designed to replace all-purpose flour and already contains a binder, such as xanthan gum or guar gum (I Like Bob’s Red Mill). This helps mimic the elasticity and texture typically found in gluten. They won’t rise quite as much, but they are still tender and tasty.

2. Alternatively, you can make high-protein bagels using oat flour. While the final product was delicious, the oat-flour bagels were moister and denser than those made with white flour. They’re still tasty, just different from traditional bagels.

How to Make Baked Protein Bagels

I’m not usually the kind of girl who makes homemade bread (or bagels!), but since I’m obsessed with cottage cheese, I had to try this recipe, and let me tell you… They do not disappoint. The best part? They are so easy. I felt like a healthy home cook rockstar 🌟 (and you will too!).

Whisking flour and baking powder together in a large bowl. — Whisk the flour and baking powder together.

Using a rubber spatula to stir the cottage cheese into the flour mixture. — Whisk the flour and baking powder together.

Once the crumbles form, trade your spatula for your hands and continue mixing the dough until it forms a smooth, slightly sticky ball that resembles fresh pizza dough.

A ball of dough on a floured surface. — Transfer the ball of dough onto a floured surface.

Four small balls of dough. — Transfer the ball of dough onto a floured surface.

Gently press a hole with your thumb in the center to form a bagel, and place it on parchment paper, adding flour as needed. Don’t aim for perfection here; let your bagels be rustic and homemade.

Brush each bagel with egg wash, dip both sides in your chosen seasoning, and place on the baking sheet.

Dough that's shaped into a bagel on parchment paper. — Press your thumb into the dough to create a bagel shape.

Baked protein bagels on a pan lined with parchment paper. — Press your thumb into the dough to create a bagel shape.

Troubleshooting + Helpful Tips

Use thick cottage cheese: The thicker the cottage cheese, the better. This will depend on the brand; some are rich and creamy, while others contain more water. Watery cottage cheese can make the dough too sticky.
Drain excess liquid: If your cottage cheese is runny, strain it through a fine mesh sieve or cheesecloth before mixing it into the dough. This will allow any excess moisture to drain away.
Flour your hands and surface: The dough will be slightly sticky. Be sure to lightly flour your hands and work surface to help make kneading and shaping easier. If things get messy, use more flour – lol.
Let them cool before slicing: These baked protein bagels firm up as they cool, so allow them to cool for 15 minutes before slicing to ensure a clean cut. If they seem a little bit wet in the center, don’t panic, just pop them in the toaster before serving.

Bagel cut in half and topped with cream cheese.

Thanks so much for reading! If you make this recipe, I would love you to give it a ★ rating below. Follow me on YouTube, Instagram, and Facebook for more healthy food inspiration. Cheers!

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4.81 from 21 votes

Baked Protein Bagels with Cottage Cheese (12g!)

Looking for an easy to make, healthy homemade bagel recipe that's packed with protein? These baked protein bagels with cottage cheese are the answer. Using just three main ingredients; flour, cottage cheese and baking powder, these high-protein (12 g!), no-boil bagels are light, fluffy and delicious. Say hello to your new favorite high-protein breakfast (or lunch!).

Course: BREAKFAST

Cuisine: American

Diet: Low Calorie

Author: Dani Spies

Prep Time10

Cook Time25

Total Time35

Servings: bagels

Calories: 167kcal

Ingredients

1 cup (120g) unbleached all purpose flour
2 teaspoon baking powder
1.25 cups 2% cottage cheese, (I love Good Culture)
1 egg, beaten, (for egg wash)
Optional toppings: everything bagel seasoning, poppy seeds, dried garlic flakes, dried onion flakes, sesame seeds, shredded asiago cheese

Instructions

Preheat the oven to 375 degrees F. Line a rimmed baking sheet with parchment paper.
In a large bowl whisk together flour and baking powder. Add the cottage cheese and mix with a fork or spatula until it looks like small crumbles.
Working in the bowl, use your hands (or a rubber spatula) and continue mixing the dough until it comes together into a ball. It will be smooth, a bit sticky, and will begin to pull away from the sides of the bowl – it will resemble fresh made pizza dough.
Transfer the dough to a lightly floured work surface and knead a few more times until no longer sticky. If needed, add an extra sprinkle of flour as you work.
Use a bench scraper or a sharp knife to divide the dough into four equal portions.
With floured hands, shape each portion into a ball, then gently press your thumb through the center to form a bagel shape. Add more flour as needed to keep it workable. Place each bagel on parchment paper.
Pour your seasoning of choice into a wide shallow bowl. Brush the top and bottom of each bagel with the egg wash and dip each side into the seasoning mixture and place on prepared baking sheet.
Bake for 25-30 minutes until fluffy and puffed up on the outside and golden brown over the top. Allow to cool for 15 minutes before slicing and serving. Enjoy!

Notes

Flour your hands and board generously. This makes it easier to work with the dough.
You can blend the cottage cheese beforehand if preferred. But I like the little craters created by the cottage cheese curds.
Don’t worry if your bagels are not perfectly shaped. They will look homemade and still taste delicious.
If your cottage cheese is loose and liquid, strain the excess liquid by scooping the cottage cheese into a fine-mesh strainer and allowing the liquid to drip off.

Storage and freezing

Let the leftover bagels cool completely, then store them in an airtight container and refrigerate them for up to five days. I have read that some people prefer to store them at room temperature because they believe refrigerating them can cause them to become stale more quickly, but I disagree. I’d be curious to hear what you think?!

For extended storage, you can individually wrap each bagel and then transfer them to a freezer-safe bag, placing them in the freezer for up to 4 months.

I recommend slicing the bagels almost all the way through before freezing, so you can easily toast them directly from frozen.

Nutrition

About Dani Spies

Dani Spies is the founder and host of Clean & Delicious; a weekly cooking show on YouTube and a healthy eating blog that celebrates real, whole foods! She takes a holistic approach to health and wellness and is loved for her approachable, down to earth style both in and out of the kitchen.

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Yum! I love this recipe.

4.81 from 21 votes