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 (12 g!), 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 of your favorite breakfast recipes. I’ve used it to make creamy Alfredo sauce, cottage cheese flatbread, high-protein pancakes, veggie-packed egg bakes, and now, high-protein baked bagels!

These high-protein bagels are 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 if you’d like an extra protein boost, serve this 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.
Baking powder: Don’t skip this! It helps the bagels rise without the need for 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: Creating a simple egg wash to brush over the top of the bagels helps give them a beautiful golden-brown sheen and allows the toppings to stick.
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 that is 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 more moist and dense 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 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.

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.

Bagel cut in half and topped with cream cheese.

WATCH + LEARN | COTTAGE CHEESE BAGEL RECIPE VIDEO

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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