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Higher Protein Einkorn Everything Bagels

March 21, 2025

If you love a classic New York bodega-style bagel, but are looking for a healthier option, then prepare to become obessed with my Higher Protein Einkorn Everything Bagels. These bagels are light and fluffy, topped with a crunchy everything bagel seasoning, and are packed with fiber and prtein, thanks to the einkorn flour. Plus, they can easily be made gluten-free, for a better-for-you bagel that everyone can enjoy!

Top view of everything bagels on parchment paper. One bagel is sliced open with creamy spread on it. A knife with more spread lies nearby, and a bowl with the same spread is partially visible in the upper right corner.

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Friends, maybe I’m biased, but after having lived in New York City for years, I can confidently say that they have the best bagels. There’s just something about a New York bagel that is fluffy on the inside, crusty on the outside, and has the perfect balance of texture and flavor. Recently, I was in Brooklyn for work (would you believe me if I said that it was my first time?) and before I left, my boys begged me to bring them back a bag of bagels from our favorite NYC deli. Sure enough, I stuffed one brown paper bag full of bagels into my carryon, and my boys were happier than ever. Happy kids = happy mom!

But because going to New York just for the bagels isn’t an option, I was inspired to find a delicious way to make them at home. But of course, since this is a Kalejunkie recipe, I wanted to make bagels with a twist. If you’ve been to my blog before, then it may come as no surprise that these days, I’m all about the protein. A high-protein diet is not only important for helping you build stronger muscles, but it also can help you to feel fuller and more satiated for longer. These bagels swap the traditional all-purpose flour for einkorn flour for a protein-packed twist.

If you’ve never had einkorn flour, it is a dense wheat flour that happens to also be high in protein and fiber. It’s a great substitute for traditional flour, in recipes where you’re wanting more of a nutritious twist.

However, if you can’t find einkorn flour, you can also susbtitute it for conventional all-purpose flour. Or, swap it out for a gluten-free 1:1 flour. Either one works well and will lead to delicious, healthy bagels that are ready in minutes!

Top view of baking ingredients on a marble surface. Includes a bowl of flour with a wooden scoop, beaten egg in a bowl with a brush, a bowl of yogurt, small dishes of salt, baking powder, and a mix of seeds and spices. — To make these bagels, you’ll need einkorn flour, baking powder, greek yogurt, kosher salt, an egg, and everything bagel seasoning (if using).

A hand uses a whisk to mix yogurt into a bowl of dry ingredients, likely flour. Various other ingredients are visible around the bowl on a light countertop, suggesting the preparation of a recipe. — To make these bagels, you’ll need einkorn flour, baking powder, greek yogurt, kosher salt, an egg, and everything bagel seasoning (if using).

The Four Ingredients You’ll Need to Make These Bagels

Einkorn Flour: Of course, these wouldn’t be einkorn bagels without the einkorn flour! Einkorn flour is a dense, wheat-based flour that also happens to be higher in fiber and protein.
Baking Powder: A little baking powder helps these bagels rise. It’s essential for helping them achieve the perfect texture.
Greek Yogurt: Greek yogurt makes these bagels light and fluffy, while also packing them full of protein. Don’t skip it!
Kosher Salt: A pinch of salt adds the perfect touch to this bagel recipe!
Egg: This is optional, but I love to brush the bagels with an egg wash, to give them that nice, golden color.
Everything But the Bagel Seasoning: This is optional, and can absolutely be omitted if you want to make plain bagels, but I love adding a sprinkle of Everything But the Bagel seasoning to turn these into everything bagels!

Next, roll the dough into a large ball, then divide it into smaller ones – you can divide it in to four balls to make larger bagels, or eight balls to make smaller ones.

How to Make These Better-For-You Bagels

To make these bagels, start by preheating your oven to 375 F. Next, prepare the bagel dough. In a large bowl or stand mixer bowl (which I recommend), mix together the flour, baking powder, and kosher salt until just combined. Then, add in the yogurt and mix again, until the ingredients come together and a dough forms. The dough should be slightly sticky but not too sticky – if it is, you can add in more flour.

Next, divide the dough into four or eight, evenly-sized balls – four if making larger bagels, and eight if making smaller-sized ones. Then, poke a hole in the center of each ball and roll them into bagels.

Four unbaked bagels topped with seed mixture on a parchment-lined baking sheet. A small bowl of seeds with a wooden spoon and a basting brush are nearby on a light-colored surface, along with a folded striped cloth. — Next, poke a hole in the top of the bagels and roll them into a bagel shape. Brush them with egg wash and top with Everything But the Bagel seasoning.

Three freshly baked everything bagels on a parchment-lined baking sheet. The bagels are topped with a variety of seeds and seasonings. In the background, there is a small jar of seasoning and stacked white plates. — Next, poke a hole in the top of the bagels and roll them into a bagel shape. Brush them with egg wash and top with Everything But the Bagel seasoning.

If using the egg, crack the egg into a bow, whisk it together, then use a pastry brush to brush the tops of each bagel. Then, sprinkle the Everything But the Bagel seasoning on top of each bagel, if using.

Transfer the bagels into the oven and allow them to bake for 25-30 minutes, until they’re golden brown. Be sure to rotate the tray halfway through, so that the bagels cook evenly. Once the bagels are done, remove them from the oven. Allow them to cool for 15 minutes, then slice and enjoy!

Once the bagels are done, allow them to cool for 15 minutes. Then, slice, serve, and enjoy!

Frequently Asked Questions

Can I substitute einkorn flour with another type of flour?

Yes! While I recommend using the einkorn flour, you can also susbtitute it with conventional all-purpose flour or gluten-free all-purpose flour.

Can these bagels be made gluten-free?

Yes, just swap out the einkorn flour for all-purpose gluten-free flour. Or, try my Best Ever Paleo Everything Bagels for a naturally gluten-free recipe!

What happens if the dough is sticky?

If the dough is too sticky, just add in more flour, one tablespoon at a time, until the dough reaches your desired consistency.

How do I shape the bagels properly?

I recommend poking a hole in the bagels and rolling them between your fingers until they reach the perfect bagel shape!

How long will these bagels stay fresh?

When stored in the fridge, these bagels will stay fresh for up to one week. When stored on the countertop, they’ll stay fresh for up to three days.

If you make this recipe, please be sure to leave a review and rating below! To see more recipes and behind the scenes, follow along on Instagram, TikTok, and Youtube! I’m also now on Pinterest, so stop by and take a look at what’s new.

** Photography by Tanya Pilgrim

Nut Free/Refined Sugar Free