Homemade Keto Greek Yogurt Bagels

Here are my keto greek yogurt bagels, with a simple almond flour base, tangy greek yogurt, and everything bagel seasoning on top for that classic bagel shop flavor.

These bagels have become my go-to breakfast since I started eating low-carb. They’re chewy, satisfying, and taste so close to the real thing that my kids don’t even notice the difference. Plus, they take less than 30 minutes from start to finish!

What Kind of Greek Yogurt Should I Use?

For keto bagels, you’ll want to stick with full-fat Greek yogurt to keep the carb count low and get the best texture. Avoid non-fat or low-fat versions since they often have added sugars and won’t give you that nice, chewy bagel consistency you’re looking for. Plain Greek yogurt is the way to go here – flavored varieties will throw off the taste and add unnecessary carbs. If your yogurt seems watery when you open it, just drain off any excess liquid before measuring it out, as too much moisture can make your bagels dense instead of fluffy.

Options for Substitutions

These keto bagels are pretty straightforward, but here are some swaps you can make:

• Almond flour: You can use coconut flour instead, but you’ll need much less – about 3/4 cup total since coconut flour absorbs more liquid. The texture will be slightly different but still works well.
• Greek yogurt: Regular full-fat Greek yogurt is best here and shouldn’t be substituted. The thick consistency and protein content are what help bind the dough together. Low-fat versions won’t work as well, and other yogurts are too runny.
• Egg: For an egg-free version, try using 3 tablespoons of unsweetened applesauce or a flax egg (1 tablespoon ground flaxseed mixed with 3 tablespoons water, let sit for 5 minutes). The bagels might be slightly less fluffy but will still hold together.
• Everything bagel seasoning: Get creative with toppings! Use sesame seeds, poppy seeds, garlic powder, or cinnamon and a sugar substitute for a sweet version. You can also skip the topping altogether for plain bagels.

Watch Out for These Mistakes While Baking

The biggest mistake with keto bagels is using cold Greek yogurt straight from the fridge, which makes the dough crumbly and hard to work with – let it sit at room temperature for 15-20 minutes before mixing for a smoother, more manageable dough.

Another common error is under-kneading the dough, so make sure you really work it for the full 3 minutes until it becomes smooth and elastic, not sticky or falling apart.

When shaping your bagels, don’t skip poking a hole in the center with your finger and gently stretching it out, because without that classic bagel shape, they’ll bake up more like biscuits than bagels.

Finally, watch your oven closely during the last few minutes of baking since almond flour can go from golden to burnt pretty quickly, and pull them out when they’re just lightly browned on top.

What to Serve With Greek Yogurt Bagels?

These keto bagels are perfect for breakfast or lunch, and they pair really well with classic bagel toppings like cream cheese, smoked salmon, and sliced red onion. I love spreading mine with herb cream cheese and adding some cucumber slices and tomato for a quick, filling breakfast. If you’re looking for something sweet instead, try topping them with almond butter and a few fresh berries, or even some sugar-free jam. They also make great sandwich bases – just slice them in half and fill with your favorite deli meats, cheese, lettuce, and mustard for an easy low-carb lunch.

Storage Instructions

Store: These bagels taste best when fresh, but you can keep them in an airtight container or zip-top bag at room temperature for up to 2 days. If you want them to last longer, store them in the fridge for up to 5 days.

Freeze: I always make a double batch and freeze half for busy mornings. Just wrap each bagel individually in plastic wrap, then place them all in a freezer bag. They’ll keep for up to 3 months and are perfect for grab-and-go breakfasts.

Toast: To bring your bagels back to life, slice them in half and pop them in the toaster. If they’re frozen, you can toast them straight from the freezer or let them thaw on the counter for about 30 minutes first. Either way, they’ll crisp up nicely and taste almost as good as fresh!

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 1150-1250
• Protein: 45-55 g
• Fat: 85-95 g
• Carbohydrates: 40-50 g

Ingredients

For the dough:

• 2 1/4 cups almond flour (I always use Blue Diamond super-fine for a smoother dough texture)
• 1 cup greek yogurt (I prefer FAGE Total 5% for the best moisture and fat content)
• 1 teaspoon baking powder
• 1/4 teaspoon salt

For the topping:

• 1 egg
• everything bagel seasoning

Step 1: Prepare Your Equipment and Mise en Place

• 1 egg
• parchment paper

Preheat your oven to 375°F and line a baking sheet with parchment paper.

Crack your egg into a small bowl and whisk it lightly with a fork—this will be your egg wash.

Having everything ready before you start mixing ensures a smooth workflow and prevents the dough from sitting too long before baking.

Step 2: Mix the Dry Ingredients and Create the Dough Base

• 2 1/4 cups almond flour
• 1 teaspoon baking powder
• 1/4 teaspoon salt
• 1 cup greek yogurt

In a medium mixing bowl, combine the almond flour, baking powder, and salt.

Whisk these together until evenly distributed, breaking up any small clumps in the almond flour.

Add the greek yogurt to the dry mixture and stir with a wooden spoon or spatula until a shaggy dough begins to form.

The yogurt provides both moisture and structure—I find that FAGE’s higher fat content creates the most tender, less dense bagels compared to lower-fat varieties.

Step 3: Knead and Shape the Dough

• dough mixture from Step 2

Knead the dough mixture for about 3 minutes using your hands, working it on the bowl or a clean surface until it becomes smooth and cohesive.

Divide the dough into 6 equal pieces and roll each piece into a ball.

Then flatten each ball into a circle about 1/4-inch thick and place them on your prepared baking sheet, spacing them about 2 inches apart.

I like to use the back of my fingers to gently press out each circle rather than a rolling pin—it helps maintain an even thickness and prevents the dough from becoming too compressed.

Step 4: Egg Wash and Season

• egg wash from Step 1
• everything bagel seasoning

Brush the top of each bagel circle generously with the whisked egg wash from Step 1, using a pastry brush or the back of a spoon.

Immediately sprinkle the everything bagel seasoning over each bagel while the egg wash is still wet so the seasoning adheres properly.

Don’t skip this step—the egg wash helps the seasoning stick and creates a slight shine on the finished bagel.

Step 5: Bake Until Golden

• shaped bagels from Step 3

Place the baking sheet in your preheated 375°F oven and bake for 18-20 minutes, until the bagels are light golden brown on top and set throughout.

The bagels will continue to firm up slightly as they cool.

Remove from the oven and let them cool on the baking sheet for 5 minutes before transferring to a wire rack or serving immediately.

Homemade Keto Greek Yogurt Bagels

Delicious Homemade Keto Greek Yogurt Bagels recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 10 minutes mins

Cook Time 25 minutes mins

Total Time 35 minutes mins

Servings 6 pieces

Calories 1200 kcal

Ingredients

  

For the dough

• 2 1/4 cups almond flour (I always use Blue Diamond super-fine for a smoother dough texture)
• 1 cup greek yogurt (I prefer FAGE Total 5% for the best moisture and fat content)
• 1 teaspoon baking powder
• 1/4 teaspoon salt

For the topping

• 1 egg
• everything bagel seasoning

Instructions

 

• Preheat your oven to 375°F and line a baking sheet with parchment paper. Crack your egg into a small bowl and whisk it lightly with a fork—this will be your egg wash. Having everything ready before you start mixing ensures a smooth workflow and prevents the dough from sitting too long before baking.
• In a medium mixing bowl, combine the almond flour, baking powder, and salt. Whisk these together until evenly distributed, breaking up any small clumps in the almond flour. Add the greek yogurt to the dry mixture and stir with a wooden spoon or spatula until a shaggy dough begins to form. The yogurt provides both moisture and structure—I find that FAGE's higher fat content creates the most tender, less dense bagels compared to lower-fat varieties.
• Knead the dough mixture for about 3 minutes using your hands, working it on the bowl or a clean surface until it becomes smooth and cohesive. Divide the dough into 6 equal pieces and roll each piece into a ball. Then flatten each ball into a circle about 1/4-inch thick and place them on your prepared baking sheet, spacing them about 2 inches apart. I like to use the back of my fingers to gently press out each circle rather than a rolling pin—it helps maintain an even thickness and prevents the dough from becoming too compressed.
• Brush the top of each bagel circle generously with the whisked egg wash from Step 1, using a pastry brush or the back of a spoon. Immediately sprinkle the everything bagel seasoning over each bagel while the egg wash is still wet so the seasoning adheres properly. Don't skip this step—the egg wash helps the seasoning stick and creates a slight shine on the finished bagel.
• Place the baking sheet in your preheated 375°F oven and bake for 18-20 minutes, until the bagels are light golden brown on top and set throughout. The bagels will continue to firm up slightly as they cool. Remove from the oven and let them cool on the baking sheet for 5 minutes before transferring to a wire rack or serving immediately.