Protein Bagels With Greek Yogurt (Easy Recipe)

These Protein Bagels With Greek Yogurt are a healthy breakfast option with a clean ingredient list. It’s the ultimate power breakfast with 18 g protein per bagel, and the best part is it’s a 5 ingredient dough mixture.

Say goodbye to regular bagels and hello this homemade protein bagels with greek yogurt recipe! With almost 18 grams of protein per bagel, they put actual bagels to shame.

if you thought making homemade fluffy bagels was some kind of intensive, full-day baking project, think again.

These Protein Bagels with Greek Yogurt are here to change the game, and yes, you can make them in under 30 minutes with just a handful of ingredients.

No waiting for dough to rise, no boiling, no fancy techniques—just mix, shape, bake, and devour. 

The secret? Greek yogurt. 

Not only does it replace the need for yeast, but it also packs these bagels with protein, making them the ultimate healthier breakfast option. And don’t worry—these are still chewy, fluffy, and ridiculously good, just like a proper bagel should be.

And of course, we’re topping them with Everything But the Bagel seasoning, because a bagel without toppings? Unacceptable. 

Whether you eat them plain, with cream cheese, or as the base for a next-level breakfast sandwich, these high-protein bagels are about to become your new go-to recipe.

If you like high protein breakfasts you may also want to try my High Protein French Toast Recipe or my Healthy Oatmeal Protein Cookies.

WHY YOU’LL LOVE THESE PROTEIN BAGELS WITH GREEK YOGURT

• High in Protein, Low in Effort – Thanks to Greek yogurt, these bagels are packed with protein without needing yeast, rising time, or complicated steps.

• No Boiling Required – Unlike traditional bagels, you can skip the water bath and still get a chewy, bakery-style bite.

• Perfectly Chewy & Fluffy – The combination of gluten-free flour, baking powder, and Greek yogurt creates the perfect texture—soft inside, golden outside.

• Super Quick & Easy – Mix, shape, and bake in under 30 minutes—perfect for busy mornings or meal prep.

• Gluten-Free & Guilt-Free – Made with gluten-free flour and simple ingredients, they’re a better-for-you option without sacrificing taste.

• Totally Customizable – Keep it classic or mix it up with cinnamon sugar, sesame seeds, cheese, or even stuffed with cream cheese.

• Pairs with Everything – Toast it, top it with cream cheese, nut butter, eggs, or avocado—whatever your bagel-loving heart desires.

• Meal-Prep Friendly – Make a batch, freeze for later, and you’ve got homemade bagels on demand.

• Healthier Than Store-Bought – No preservatives, unnecessary additives, or extra sugar, just wholesome ingredients and high-protein goodness.

BENEFITS OF THIS HIGH PROTEIN BAGEL RECIPE

• Packed with Protein – Thanks to Greek yogurt, each bagel delivers a solid protein boost, making it a more filling and energizing breakfast.

• No Yeast, No Waiting – Unlike traditional bagels, this recipe requires zero rising time—just mix, shape, and bake!

• Gluten-Free Friendly – Made with gluten-free flour, so you can enjoy that chewy bagel texture without the gluten.

• Lower in Carbs, Higher in Nutrients – With fewer refined carbs than standard bagels, these are more balanced for blood sugar control and satiety.

• Supports a Healthy Lifestyle – A great high-protein, nutrient-dense alternative to store-bought bagels, perfect for meal prep, weight management, and muscle recovery.

SIMPLE INGREDIENTS FOR THE 3 INGREDIENT HIGH PROTEIN BAGELS

You will need the following main ingredients listed below to make the gluten free bagels (the exact measurements, nutritional data and full recipe are in the printable recipe card at the bottom of the post):

• Gluten-free all purpose flour – you can also use whole wheat flour, regular all-purpose flour, or self-rising flour if you omit the baking powder. Do not use coconut flour in this recipe it will not work as a replacement.
• Baking powder
• Salt
• Plain greek yogurt
• Whole egg or egg white wash
• Bagel seasoning – you can make your own with a blend of poppy seeds, bacl sesame seeds, white sesame seeds, chia seeds, dried minced garlic, dried minced onion, and sea salt.
• Optional – unflavored protein powder, whey protein powder, cottage cheese, vegan greek yogurt, sunflower seeds, etc.

HOW TO MAKE THE HOMEMADE BAGELS

In a large bowl, mix together the gluten-free all purpose flour, baking powder and salt until well combined. Add in the greek yogurt and stir until bagel dough forms.

Divide the dough into 2 equal pieces and shape each piece into a smooth dough ball on a lightly floured work surface.

Roll each ball of dough until it becomes a rope, making it as smooth and even as possible. Pinch the ends together to form a circular shape, creating a bagel shape.

Preheat air fryer for 5 minutes at 350 degrees F. Then spray the greek yogurt bagels with non-stick spray or olive oil (can also use egg whites or a beaten egg for egg wash), top with bagel seasoning and air fry for 8 minutes.

Flip them over and air fry for another 2-3 minutes, or until golden brown. Serve warm with toppings of your choice.

DIFFERENT VARIATIONS FOR THIS PROTEIN BAGEL RECIPE

There are many different flavors of homemade bagels that you can try making at home! Here are some ideas:

1. Plain Typical Bagel – the classic flavor! Brushed with egg wash or egg whites so the bagels get golden brown.
2. Everything Traditional Bagel – topped with a mixture of poppy seeds, sesame seeds, dried garlic, dried onion, and salt. This is the original recipe.
3. Cinnamon Raisin Bagels – with a sweet cinnamon brown sugar flavor and juicy raisins.
4. Blueberry Bagels – with fresh or dried blueberries mixed into the dough.
5. Asiago Cheese Bagels – with chunks of Asiago cheese baked into the dough.
6. Jalapeño Cheddar Bagels – with diced jalapeños and shredded cheddar cheese mixed into the dough.
7. Garlic Bagels – with fresh minced garlic mixed into the dough.
8. Chocolate Chip Bagels – with mini chocolate chips mixed into the dough. Could also add peanut butter to mix throughout to make peanut butter chocolate chip bagels.
9. Onion Bagels – with minced onions mixed into the dough. Could even throw some bacon bits in there.
10. Sun-Dried Tomato Bagels – with chopped sun-dried tomatoes mixed into the dough.

The possibilities are endless! Experiment with different flavors and toppings to create your own unique bagel creations.

STORING LEFTOVER PROTEIN BAGELS WITH GREEK YOGURT

• Room Temperature: Store in an airtight container for up to 2 days.
• Refrigerate: Keep in the fridge for up to 5 days for freshness.
• Freeze: Slice first, wrap individually, and store in a freezer-safe bag for up to 3 months.
• Reheating: Toast in a toaster, air fryer (best option!), or oven. Microwave for a quick fix but expect a softer texture.

FAQS

CAN I BAKE THESE PROTEIN GLUTEN-FREE BAGELS IN THE OVEN?

Yes, if you don’t have an air fryer you can make them in the oven. Preheat oven to 350F and line a baking sheet or baking tray with parchment paper.

The cooking process is very similar, you will still follow all the same directions on a well floured surface. The only difference will be the cooking time in the oven.

Bake the bagels for 20-25 minutes or until bagels are cooked all the way through. You can crisp the outside of your bagel at the end by toasting them, or turning your oven up to 500F and baking them for 1-2 minutes.

WHAT ARE SOME FAVORITE TOPPINGS FOR THESE PROTEIN BAGELS WITH GREEK YOGURT?

Try classic cream cheese, almond butter, avocado, smoked salmon, or even a drizzle of honey for the ultimate flavor boost!

CAN I USE SELF-RISING FLOUR INSTEAD OF GLUTEN-FREE FLOUR IN THESE 2 INGREDIENT BAGELS?

Yes! Self-rising flour works great in place of the flour and baking powder.

CAN I USE COTTAGE CHEESE INSTEAD OF FULL-FAT GREEK YOGURT?

Yes! Cottage cheese bagels work well, but you’ll need to blend it smooth before mixing.

ARE THESE PROTEIN BAGELS WITH GREEK YOGURT A GOOD HIGH-PROTEIN BREAKFAST RECIPE?

Yes! These bagels are packed with protein and make a filling, nutritious breakfast option.

Other Healthy Breakfast Recipes You May Like To Try!

• Easy 3 Ingredient Mini Gluten Free Bagel Bites
• Overnight Keto Chia Seed Pudding
• Vegan Banana Chocolate Chip Sheet Pan Pancakes
• The Best Fluffy Plant Based Cinnamon Rolls
• Tiramisu Protein Baked Oatmeal
• Banana Bread Protein Baked Oatmeal
• Meal Prep Egg White Breakfast Sandwiches
• Freezer Bacon Breakfast Sandwiches
• Tiramisu Chia Pudding
• Chocolate Peanut Butter Baked Oatmeal
• Mexican Veggie Breakfast Skillet
• Scrambled Oats Recipe
• Microwave Egg White Oatmeal
• Air Fryer Cottage Cheese Toast
• Air Fryer Frittata Recipe

IF YOU TRIED THESE PROTEIN BAGELS WITH GREEK YOGURT PLEASE LEAVE A COMMENT IN THE COMMENT SECTION AND STAR RATING. I LOOK FORWARD TO SEEING YOUR CREATIONS! YOU CAN PIN THESE EASY BAGELS ON PINTEREST OR SHARE ON INSTAGRAM BY TAGGING @basicswithbails and #basicswithbails