High-Protein Bagels Made with Greek Yogurt
These high-protein bagels are a total game changer—soft, chewy, and packed with satisfying goodness—and all without any yeast, boiling, or fancy equipment. They’re made with just a few simple staples (Greek yogurt and white whole-wheat flour do the heavy lifting here!) and come out perfectly golden every time.

These better-for-you bagels pack 10 grams of protein, 4 grams of fiber, and a whole host of vitamins and minerals. That’s because they’re made with whole-grain flour, which contains more fiber and minerals than standard flour; chia seeds, which are filled with fiber and omega-3 fats; and protein-rich Greek yogurt.



Now that’s what I call ba-GOALS!
- High in protein, low in fuss: No yeast, no rising time—just mix, roll, and bake!
- Totally customizable: Sprinkle on everything bagel seasoning, sesame seeds, or cinnamon-sugar for sweet or savory versions.
- Meal-prep friendly: Make a batch, slice ‘em and freeze then toast for grab-and-go breakfasts or sandwiches.
- Nutritious twist: Each bagel delivers protein and fiber thanks to the yogurt, chia seeds, and whole-wheat flour.

A few topping suggestions, if I may…
For a sweet start to your day, I recommend my 2-Ingredient Blueberry Chia Jam or Dark Chocolate Peanut Butter Spread. If you prefer to use your bagel as a vehicle for a protein-packed meal, layer on my Creamy & Crunchy Chicken Salad, Tarragon Chicken Salad, or Mediterranean Chopped Salad. You can also try this Cacio e Pepe Egg Salad, Lightened-Up Egg Salad, or Creamy Tuna Salad.
Note: These bagels freeze wonderfully; read the note section below for full details on freezing and storage, as well as alternative flours you can use!


Love these bagels? Try my Cinnamon Raisin Protein Bagel for a little variety.

High-Protein Bagels Made with Greek Yogurt
Ingredients
- 2 cups white-whole wheat flour
- 1 tablespoon baking powder
- 1 tablespoon chia seeds
- 1 ½ teaspoon kosher salt
- 2 cups non-fat plain Greek yogurt, thicker brands work best*
Instructions
- Preheat oven to 350°F. Line a baking sheet with parchment paper and set aside.
- Combine the flour, baking powder, chia seeds, and salt in a large bowl. Add the yogurt and mix until all the ingredients are incorporated into a batter.
- Using your hands, press and fold the flour into the yogurt until all of the pieces come together to form an elastic dough.
- While at first the dough will be fussy and crumbly, after about 1 minute of pressing and folding it will come together. Divide into 8 balls.
- One at a time, roll each ball between your palms and form into a long rope (if it breaks apart, just squish it back together).
- Lay the rope on the parchment paper and form it into a circular shape, cinching the ends to complete a closed bagel. Leave space between each bagel on the baking sheet so they’re not touching.
- Dip the tops into any preferred seasonings, if desired.
- Place in the oven and bake for 25 minutes. Let cool before slicing.
Notes
• Leftover bagels can be kept in a sealed bag for up to 3 days in the refrigerator. • You can also freeze your bagels for up to 3 months. First, let them cool. Then slice them and wrap each one individually (both halves together) and store the batch in the freezer in a freezer bag or sealed container. • To thaw your frozen bagels, either set on the counter to naturally thaw at room temperature (one at a time, as needed), or defrost in the microwave, heating in 30-second intervals until soft and warmed. Or, you can toast in the oven directly from the freezer since they’re already sliced. Works great!

Can you use vegan plain yogurt?
Hi! We haven’t tested it with vegan yogurt yet, but we did a quick search and found positive reviews for coconut and soy yogurt. You could try a few different brands of these types and see if they work. If you do, we’d love to hear back from you. Greek yogurt is thick, rich in protein and provides a little tang, which is why it works perfectly in my bagel recipe. (Note: Neither option offers as much protein as Greek dairy yogurt, but of the two, soy has more protein than coconut.) Good luck and let us know if you decide to try it.
—Team Joy
Would bread flour work for this recipe?
Yes, bread flour would work perfectly! We hope you love the recipe as much as we do, Sharon!
— Team Joy
I don’t like Chia seeds anything to substitute or just leave out
Just leave them out! You don’t need to replace them with anything.
— Team Joy
Does it have to be nonfat yogurt?
Hi Nycke!
We haven’t tested this recipe with a higher fat Greek yogurt, but after researching and asking a few chef friends, here’s what we found:
• The recipe should work with all fat varieties of Greek yogurt, as long as it has a thicker consistency (Fage is a good brand to consider). Remember to drain the liquid before measuring.
• Thick dairy-free (vegan) Greek-style yogurt should also work. You may want to look into Kite Hill brand.
If you do try this recipe with a dairy-free yogurt, please let us know how the bagels turn out!
—Team Joy
I cannot do dairy & most dairy-free yogurts are runny at best. Could I use mayo as a substitute or what would you recommend? Thank you, Joy!
Hi Frances. Unfortunately, mayo won’t work for these bagels.
We haven’t had a chance yet to experiment with dairy-free yogurt in this recipe, but from our research, thicker brands seem to work. You may want to look into Kite Hill brand if you haven’t tried it. If you do decide to give it a shot, please let us know how it turns out.
These were easy to make and almost like a real bagel. I’ll make them again!
Hi Donna. So glad you’re enjoying them. Don’t forget to try the Cinnamon Raisin and Everything versions, too!
—Team Joy
I loved this recipe! The bagels are delicious and they were super easy to make. I used 1 cup whole wheat flour and 1 cup all-purpose flour. I will definitely make these again.
Hi Mary. Yay! We’re so happy to hear you’re enjoying Joy’s protein bagels, and that you made an easy ingredient tweak that works for you. We recommend trying Joy’s Blueberry Chia Jam or Cherry Chia Jam as a topping—so delicious. Let us know if you decide to give either one a shot.
—Team Joy
Delicious! Flavored in pairs- I dipped a few in cinnamon and put home grown fresh blueberries in a few. Haven’t tasted them yet, but the poppyseed, sesame seed, garlic powder and black pepper one was great (I am out of everything bagel seasoning but didn’t want to wait to make these).
How do you recommend storing them?
Hi Kathy!
That sounds amazing!! We love the idea of using fresh blueberries and different seasonings. Please keep us posted! ❤
Thank you so much for asking about how to store the bagels! We’ve just updated our notes section above with all the details.
— Team Joy
Thanks for this wonderful recipe! Wondering if you can also put the bagels in boiling water before baking?
Hi Denise! Joy has never tried boiling her protein bagels prior to baking them, so unfortunately, she’s not sure if it will work with this type of special dough. If you do give it a try, please let us know how they turn out. And maybe consider boiling just one or two as a test… this way, if it doesn’t work out, the rest will be saved!
-Alison
I made these two days ago… so simple and DELICIOUS! My husband raved about them. I promised to make them again!
Karen, I just read this and have the biggest smile on my face!! Hooray for protein bagels! Thanks for taking the time to leave such a wonderful review 😉
These have become a weekly addition to our menu. I added hemp seeds for added protein and you can’t even tell! Next is to make them with my grandchildren this week. I’m imagining that they’ll dip them in cinnamon sugar!
Hi Karen, so happy to hear you’re enjoying the bagels, and we love your healthy addition of hemp seeds. Hoping your grandkids devour them! We suggest serving Joy’s chia jam as a naturally sweet spread!
—Donna
Delicious bagels! This recipe is easy to make and requires few ingredients. I made them with Fage Greek yogurt. I had been craving a bagel but I didn’t want all the carbs that a traditional bagel has and I try to limit my fat and sugar intake. These bagels hit the spot and are much healthier than traditional bagels. Thank you, Joy, for bringing us healthier versions of the foods we love!
Hi Lane, What a nice note! We’re so glad you enjoyed these Protein Bagels…they are super easy to make and made with tasty, nutrient-packed ingredients! — Eliza (Team Joy)
Amazing Thank You So Much Joy ❤️❤️
You’re so welcome, Joanne! xx
Joy, can we use Kodiak instead of whole wheat flour? Thanks
I did make these once before with ww flour, mine were a little flat but tasted good.
Hi Chris, great Q! Yes, you can swap in Kodiak pancake mix (for the whole wheat flour), but since Kodiak already has leavening mixed in, you should reduce the baking powder a bit. I’d drop it from 1 tablespoon to 2 teaspoons when using Kodiak — that gives you a nice lift without over-puffing or creating an “off” taste. I’ve never tried this swap before, so if you make the bagels with this flour swap, please let me know how they turn out!
This truly sounds delicious and EASY…anxious to try it! A guilt free bagel…yum!
Thanks, Lynda! If you choose to give this recipe a try, let us know what you think! We think you’ll love them!— Eliza (Team Joy)
These bagels are easy to make and delicious! And I don’t feel guilty eating them! Thank you Joy for this recipe!
So glad you love this recipe, Beth! You’re welcome! — Eliza (Team Joy)
Been making these for years. I experimented with regular yogurt, it’s doable however you will need to add lots more flour. I zhoosh it up adding dried cranberries and cinnamon inside. My recipe has 375 oven which I think cooks it better for 25 minutes. Love the fact it is all whole wheat.
Hi Theresa! Thank you for your helpful comment. Dried cranberries and cinnamon sounds like a delicious addition.— Eliza (Team Joy)
Do you have a video of Step 3?
Hi Jessica! Here’s an Instagram video Joy made: https://www.instagram.com/reel/DEyF6WHuyQk/! Hope this helps! — Eliza (Team Joy)
These could not be easier and they’re delicious. I have made them twice already. Perfect with a spread of almond butter!
Hi Anne! Love this! These bars are all about simple, wholesome deliciousness, so we’re thrilled they’ve already made it into your regular rotation. And yes… a swipe of almond butter on top is chef’s kiss perfection. Thanks for sharing your sweet feedback!— Eliza (Team Joy)
These sound amazing. Do you think they would work with gluten free flour?
Hi Lynette! Yes! A gluten-free baking flour that’s a 1-to-1 swap for all-purpose flour works well here. Just be sure to choose a blend specifically labeled as a one-for-one replacement.Joy wouldn’t recommend oat flour or almond flour for this recipe…they don’t create the same doughy, bagel-like texture. If you go the gluten-free route, the results will be best with a true GF baking blend. Let us know how they turn out!— Eliza (Team Joy)
Two cups of yogurt? Or two containers ?!? It’s very sticky!
Hi Diane!! Two cups… and you may want to add more flour…. just keep kneading it! — Eliza (Team Joy)
Perfect! Thank you!
Best bagels ever!! Used whole wheat flour. A little extra flour so the dough was more workable, just a sprinkle on the board I was rolling them on. Very moist and delicious.
So happy to hear that! Thank you for sharing, Diane! Whole wheat flour is a great swap, and that little extra sprinkle to make the dough easier to handle is such a smart tip. Love that they turned out moist and delicious…enjoy every bite!— Eliza (Team Joy)
I still can’t get over how Delicious these bagels were ! Wow ! You are amazing Joy and i have truly loved everyone of your delicious easy amazing recipes! I can’t begin to thank you enough ! I couldn’t imagine it really tasting like a bagel. And i must say ~ Delicious, healthy , protein packed goodness and very easy !! I am so very impressed, I’ll be telling everyone and definitely making them again soon. 5 stars ⭐️ ⭐️⭐️⭐️⭐️
Michele, this comment just made my day!! Thank you so much for taking the time to share this…. and for being apart of my community!! xx
Thank you for another great useful recipe! I’ve deprived myself of bagels for awhile, but this wholesome easy recipe has changed that. I use them as a lunch bagel … toasted with a slice of avocado and sometimes a slice of cheese. Yummy! I usually make a double batch and freeze. I take them out of the freezer a few at a time and allow to thaw in ref.
Love the practicability and healthiness of your recipe. Another keeper!
Hi Becky! So glad to hear that you love this recipe! It’s definitely a keeper! And thank you for sharing your freezer tip. Such a good hack for a bagel anytime the craving strikes!— Eliza (Team Joy)