Almond Flour Greek Yogurt Bagels
Why You’ll Love These Almond Flour Greek Yogurt Bagels
These Almond Flour Protein Bagels have been on constant rotation in our house lately because they’re just that good! Soft, chewy and packed with protein, these healthy bagels are made with almond flour, Greek yogurt and cottage cheese for an easy gluten-free breakfast or snack that actually keeps you full. If you’ve been looking for high-protein bagels that are gluten-free, grain-free, low-carb and keto-friendly, this recipe checks all the boxes. And the texture? They’re soft inside with a golden, crusty exterior and chewy texture.
I tested several different ingredient combinations before landing on this version, and the texture and flavour turned out exactly how I hoped. Most almond flour bagel recipes use Greek yogurt, which adds great moisture and protein, but I wanted to create an even higher protein bagel recipe without making them dry or dense. With cottage cheese having such a moment lately, I decided to try blending it into the dough along with the yogurt and it worked perfectly! The key is blending the cottage cheese and Greek yogurt until completely smooth using a food processor or high-speed blender. This gives the bagels a much softer, smoother texture and helps create that classic chewy bagel feel.
Not only do these Almond Flour Greek Yogurt Bagels taste delicious, but they’re also surprisingly simple to make. The recipe comes together easily with wholesome ingredients and no yeast required. They’re naturally gluten-free and grain-free, while still being satisfying, protein-packed and lower in carbs than traditional bagels. They also toast beautifully, making them perfect for meal prep breakfasts throughout the week.
I chose to top mine with classic everything bagel seasoning, but these homemade protein bagels are incredibly customizable. You can keep them plain, make sesame bagels, or even turn them into cinnamon raisin bagels for a sweeter option. My favourite way to enjoy them is toasted with cream cheese, but they also make amazing breakfast sandwiches or quick high-protein lunches.
If you love almond flour baking, try my Almond Flour Biscuits with Rosemary for a cozy gluten-free side or maybe something sweeter like my Gluten Free Double Chocolate Cookies. Alternatively, maybe you want to find more high-protein breakfast recipes. Check out my high-protein breakfast recipes here: High-Protein Breakfasts.

Ingredient Tips and Substitutions
A few things to keep in mind:
- Greek Yogurt – Greek yogurt is a staple ingredient for these bagels. It adds protein as well as acid to the dough to make it expand beautifully. I recommend plain, full-fat greek yogurt for this recipe.
- Cottage cheese – I love the viral greek yogurt bagels, but I wanted to find a way to add even MORE protein. Hence, cottage cheese! Cottage cheese has 18g of protein in just half a cup! This, along with the greek yogurt makes for the perfect, gluten-free, high-protein bagels.
- Almond flour – The only flour you need is almond flour. We are keeping this one real simple! Almond flour is naturally gluten-free, grain-free and lower in carbs which is why I love it so much. You will need almond flour, not almond meal for this recipe.
- Tapioca flour – You will need a small amount of tapioca flour for dusting and shaping the bagels. The dough will be quite sticky, so it helps to dust your hands before forming the bagels. You can also use rice flour if you are not grain-free.
- Everything Bagel Seasoning – It’s the star of the show! Everyone loves Everything Bagel Seasoning! You can sprinkle on however much you prefer. I like lots of seasoning, so I sprinkle it on generously!
How to Make High-Protein Gluten-Free Bagels
Step 1: Blend the greek yogurt and cottage cheese.
Add the greek yogurt and cottage cheese to a food processor and blend on medium speed until combined very smooth in texture (no cottage cheese lumps left).

Step 2: Add the dry ingredients.
Add the almond flour, baking powder and salt to the food processor and blend on low or pulse until a dough-like consistency forms. Alternatively, you can scrape the yogurt and cottage cheese mixture into a medium-sized mixing bowl and mix in the dry ingredients that way.

Step 3: Portion out the dough.
Preheat the oven to 350F and line a baking sheet with parchment paper or a silicone matt. Turn the bagel dough onto a lightly floured surface, using either tapioca or rice flour, and roll the dough around with the palm of your hand to let it absorb some of the flour. Do this a couple of times until it’s just not quite as sticky. Then, flatten into.a disk shape and cut into 4 equal parts using a bench scraper or knife.

Step 4: Shape the bagels.
With each of the four sections, roll the dough into a ball and then polk a hole through the middle with your finger. Do not flatten them at all! They will spread when they bake. If you flatten them before baking you will end up with pancake bagels.

Step 5: Brush, season and bake.
Whisk the egg plus 1 teaspoon of water in a small bowl. Add the bagels to the prepared baking sheet and brush the tops and sides all over with egg wash. Season the tops generously with Everything Bagel Seasoning and bake in the preheated oven for 25 minutes until golden brown. Let them cool completely before slicing open.


Expert Tips for the Best Low-Carb Almond Flour Bagels
- Blend the cottage cheese and yogurt until completely smooth or the texture can become lumpy and hard to mix.
- Use fine almond flour, not almond meal.
- Dust your hands generously with tapioca flour because the dough is sticky. This will make it easier to work with.
- Let the bagels cool completely before slicing or they may crumble.
- Toast leftovers for the best texture. They crisp up great in the toaster! Slather a thick layer of cream cheese on top for the best flavour experience!
Serving Pairs and Suggestions
Here are some of my favourite ways to eat Almond Flour Greek Yogurt Bagels:
- Toasted and topped with a generous layer of regular cream cheese or a herbs and garlic cream cheese.
- Toasted with smashed avocado and a fried egg for extra protein!
- Toasted as a sandwich with mayonnaise, mustard, sliced meat, cheese and lettuce.
- Toasted and topped with plain cream cheese, wild salmon lox, fresh dill, capers and a squeeze of lemon.
- Toasted with just butter as a more simple option if serving as a side to soup or salad.
FAQ:
Yes, you can. They just won’t have quite as much protein!
If you don’t have a food processor you can also use a high-powered blender or hand blender to blend the cottage cheese and yogurt. Essentially, the most important thing is that the cottage cheese curds get full broken down. If they remain chunky it will affect the overall texture of the bagels.
Yes! They toast beautifully. I usually have to put them down twice, but then they’re perfect. Especially topped with the classic; cream cheese. Yum!
Be very careful when cutting them in half; don’t cut yourself!
I recommend storing them in the fridge in an air tight container. It will make them kind of dense, but once they’re toasted again, they’re like brand new! Delicious.
If they are stored in an air-tight container in the fridge, they last for about 3-4 days. As time goes on they may tend to dry out. So it’s better to eat them sooner than later. And always toast them for the best results!
Yes! They are freezer-friendly. I recommend storing in an air tight container in the freezer for up to 1 month.
If you’re on a keto diet aiming for 50 net carbs per day, then yes! Each bagel has about 34 grams of fat and only 9 net grams of carbs, making them keto friendly.

Almond Flour Greek Yogurt Bagels
Equipment
- 1 Food Processor
- 1 Baking Sheet
Ingredients
- 1/2 cup plain greek yogurt
- 1/2 cup full-fat cottage cheese
- 2 cups almond flour
- 1 tablespoon baking powder
- 1/2 teaspoon sea salt
- tapioca flour for dusting
- 1 egg + 2 tsp water for basting
- everything bagel seasoning for topping
Instructions
- Preheat the oven to 350F and line a baking sheet with parchment paper.
- Add the greek yogurt and cottage cheese to the bowl of a food processor and blend on medium speed until cottage cheese curds are completely broken down and smooth, about 15 seconds.
- Add the almond flour, baking powder and salt and blend again until a sticky dough comes together.
- Dust the counter top with tapioca flour and scoop out the dough with a spatula onto the dusted surface.
- Dust your hands and then knead very gently a couple of times until the surface is no longer sticky, incorporating some of the tapioca flour.
- Form the dough into a ball and flatten slightly. Using a bench scraper, cut the dough into four equal parts.
- Form each section into a bagel shape, placing them on the baking sheet when done. My technique is to roll each one into a ball, place it on the baking sheet, flatten it very slightly and then make a hole in the centre.
- Whisk the egg and water in a small bowl and then baste the tops and sides of the bagels. Sprinkle them all over with Everything Bagel Seasoning.
- Bake in the preheated oven for 25 minutes. Let cool for at least 30 minutes before cutting into them.