Everything Bagel Protein Bagels

I’ll be honest—I used to think making bagels from scratch was something only professional bakers could pull off. All that yeast, the boiling water, the waiting around for dough to rise. Who has time for that on a Tuesday morning?

Then I discovered this recipe, and it changed everything. These bagels use just three main ingredients (okay, plus a few extras for flavor), and you don’t need any fancy skills or equipment. No yeast, no boiling, no waiting. The secret? Greek yogurt. It sounds weird, but trust me—it works. The yogurt gives you that chewy bagel texture while sneaking in extra protein, which means you can feel slightly better about eating two in one sitting.

What Kind of Yogurt Should I Use?

For these protein bagels, Greek yogurt is your best bet since it’s thicker and has more protein than regular yogurt. Full-fat, low-fat, or even fat-free Greek yogurt will all work fine, so just use whatever you have on hand or prefer. If your yogurt seems really watery or has liquid sitting on top, give it a quick stir or drain off that excess liquid before measuring it out. Some people like to use Icelandic yogurt (skyr) as well, which works great because it’s even thicker and has tons of protein. Just avoid using regular thin yogurt or drinkable yogurt, as they won’t give you the right dough consistency.

Options for Substitutions

While this recipe is pretty straightforward, here are some swaps you can make:

• Flour: All-purpose flour works best here and shouldn’t be substituted with almond or coconut flour, as they won’t give you that proper bagel texture. If you need a whole grain option, you can replace up to half the flour with whole wheat flour, but expect a denser result.
• Yogurt: Greek yogurt is ideal for this recipe because of its thick consistency and protein content. Regular yogurt is too thin and will make your dough sticky and hard to work with. If you only have regular yogurt, strain it through cheesecloth for a few hours first.
• Everything bagel spice: Don’t have everything bagel seasoning? Make your own by mixing sesame seeds, poppy seeds, dried minced garlic, dried minced onion, and coarse salt. You can also use plain sesame seeds, sea salt, or skip the topping entirely for plain bagels.
• Egg: The egg wash gives bagels their golden color, so if you don’t have eggs, brush the tops with a little milk or melted butter instead. The bagels will still bake up nicely, just with a lighter color.
• Baking powder: Baking powder is essential here – it’s what makes these bagels rise without yeast. Don’t substitute with baking soda, as it won’t work the same way.

Watch Out for These Mistakes While Baking

The biggest mistake people make with these bagels is over-kneading the dough, which activates too much gluten and creates tough, chewy bagels instead of soft ones – stick to just 2 minutes of gentle kneading and no more.

Another common error is making the center holes too small, since they’ll close up quite a bit during baking, so aim for a hole that’s at least 1-2 inches wide using your thumb or the handle of a wooden spoon.

Don’t skip the egg wash step, as it’s what gives your bagels that golden, shiny finish and helps the everything bagel seasoning actually stick to the surface instead of falling off.

Finally, resist the urge to slice into them right away – letting the bagels cool for at least 10 minutes helps them firm up and prevents them from getting gummy when you cut through them.

What to Serve With Protein Bagels?

These protein bagels are perfect for breakfast or lunch, and they pair well with just about any bagel topping you love. I like to slather mine with cream cheese and top it with smoked salmon, red onion, and capers for a classic deli-style meal. If you’re looking for something simpler, try peanut butter and sliced banana, or go savory with avocado, a fried egg, and a sprinkle of red pepper flakes. These bagels also make great sandwich bases – pile on some turkey, lettuce, tomato, and mustard for an easy lunch that’ll keep you full for hours.

Storage Instructions

Store: Keep your protein bagels in an airtight container or zip-top bag at room temperature for up to 2 days, or in the fridge for about 5 days. They taste great either way, though I find they stay a bit softer when stored at room temperature.

Freeze: These bagels are perfect for freezing! Just slice them in half before freezing so you can pop them straight into the toaster. Store them in a freezer bag with as much air pressed out as possible, and they’ll keep for up to 3 months.

Toast: Whether fresh or frozen, these bagels are best when toasted. If frozen, you can toast them directly from the freezer without thawing. Just add an extra minute or two to get them nice and crispy on the outside while warming through.

Estimated Nutrition

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

• Calories: 2100-2250
• Protein: 75-85 g
• Fat: 30-40 g
• Carbohydrates: 400-420 g

Ingredients

For the dough:

• 3.25 cups flour (I always use King Arthur all-purpose flour)
• 3 cups yogurt (thick Greek style works best for dough texture)
• 4 tsp baking powder
• 2 tsp salt
• 1/2 tsp garlic powder

For the wash:

• 1 egg (beaten with a splash of water for a golden crust)

For the coating:

• 2 cups everything bagel spice (I prefer Trader Joe’s brand for this)

Step 1: Prepare Your Workspace and Oven

Preheat your oven to 400°F and line a baking sheet with parchment paper.

This gives your oven time to reach temperature while you prepare the dough, ensuring even baking from the start.

Step 2: Mix the Dough Base

• 3.25 cups flour
• 4 tsp baking powder
• 2 tsp salt
• 1/2 tsp garlic powder
• 3 cups Greek yogurt

In a large mixing bowl, combine the flour, baking powder, salt, and garlic powder.

Whisk these dry ingredients together for about 30 seconds to evenly distribute the leavening agents.

Add the Greek yogurt and stir with a wooden spoon or your hand until a shaggy dough forms—this should take just a minute or two.

The dough will look rustic and slightly sticky, which is exactly what you want.

I find that using thick Greek yogurt (not regular yogurt) gives you the best texture, as the extra protein helps hold everything together without needing eggs in the dough itself.

Step 3: Knead and Shape the Bagels

Turn the dough out onto a lightly floured surface and knead for 2 minutes until it becomes smooth and slightly less sticky.

Divide the dough into 9-12 equal portions (I aim for 10 for a nice size) and roll each into a ball.

Working with one ball at a time, use your thumb or a wooden spoon handle to poke a hole through the center of each ball, gently stretching it into a bagel ring shape with about a 2-inch hole in the middle.

The dough is forgiving, so don’t worry about making them perfect—rustic bagels are charming.

Step 4: Apply Egg Wash and Seasoning

• 1 egg, beaten with water
• 2 cups everything bagel seasoning

Beat the egg with a splash of water to create your egg wash.

Place all your shaped bagels on the prepared baking sheet.

Brush the top and outer edges of each bagel generously with the egg wash—this will give them a beautiful golden crust.

Immediately sprinkle the everything bagel seasoning over the wet egg wash so it adheres properly.

I recommend doing this in sections rather than all at once, so the egg wash doesn’t dry out before you add the seasoning.

Step 5: Bake Until Golden

Place the baking sheet in your preheated 400°F oven and bake for 28-32 minutes, until the bagels are golden brown on top and the bottoms are firm when tapped.

The bagels should sound slightly hollow when done.

If the tops are browning too quickly, you can tent the sheet loosely with foil for the last 5-10 minutes.

Step 6: Cool and Serve

Remove the bagels from the oven and let them cool on the baking sheet for 5-10 minutes before transferring to a cooling rack or serving board.

This short cooling period allows the structure to set while they’re still warm and most enjoyable.

Serve with your favorite spreads or simply enjoy them plain—the everything bagel seasoning provides plenty of flavor on its own.

Everything Bagel Protein Bagels

Delicious Everything Bagel Protein Bagels recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 30 minutes mins

Total Time 45 minutes mins

Servings 10 bagels

Calories 2175 kcal

Ingredients

  

For the dough::

• 3.25 cups flour (I always use King Arthur all-purpose flour)
• 3 cups yogurt (thick Greek style works best for dough texture)
• 4 tsp baking powder
• 2 tsp salt
• 1/2 tsp garlic powder

For the wash::

• 1 egg (beaten with a splash of water for a golden crust)

For the coating::

• 2 cups everything bagel spice (I prefer Trader Joe's brand for this)

Instructions

 

• Preheat your oven to 400°F and line a baking sheet with parchment paper. This gives your oven time to reach temperature while you prepare the dough, ensuring even baking from the start.
• In a large mixing bowl, combine the flour, baking powder, salt, and garlic powder. Whisk these dry ingredients together for about 30 seconds to evenly distribute the leavening agents. Add the Greek yogurt and stir with a wooden spoon or your hand until a shaggy dough forms—this should take just a minute or two. The dough will look rustic and slightly sticky, which is exactly what you want. I find that using thick Greek yogurt (not regular yogurt) gives you the best texture, as the extra protein helps hold everything together without needing eggs in the dough itself.
• Turn the dough out onto a lightly floured surface and knead for 2 minutes until it becomes smooth and slightly less sticky. Divide the dough into 9-12 equal portions (I aim for 10 for a nice size) and roll each into a ball. Working with one ball at a time, use your thumb or a wooden spoon handle to poke a hole through the center of each ball, gently stretching it into a bagel ring shape with about a 2-inch hole in the middle. The dough is forgiving, so don't worry about making them perfect—rustic bagels are charming.
• Beat the egg with a splash of water to create your egg wash. Place all your shaped bagels on the prepared baking sheet. Brush the top and outer edges of each bagel generously with the egg wash—this will give them a beautiful golden crust. Immediately sprinkle the everything bagel seasoning over the wet egg wash so it adheres properly. I recommend doing this in sections rather than all at once, so the egg wash doesn't dry out before you add the seasoning.
• Place the baking sheet in your preheated 400°F oven and bake for 28-32 minutes, until the bagels are golden brown on top and the bottoms are firm when tapped. The bagels should sound slightly hollow when done. If the tops are browning too quickly, you can tent the sheet loosely with foil for the last 5-10 minutes.
• Remove the bagels from the oven and let them cool on the baking sheet for 5-10 minutes before transferring to a cooling rack or serving board. This short cooling period allows the structure to set while they're still warm and most enjoyable. Serve with your favorite spreads or simply enjoy them plain—the everything bagel seasoning provides plenty of flavor on its own.