Homemade Whole Wheat Bagel Recipe! (2024)

by Faith VanderMolen

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If you've never made bagels before, I hope this Homemade Whole Wheat Bagel Recipe gives you the confidence you need to give them a try. If I can do it, so can you!

Homemade Whole Wheat Bagel Recipe! (1)

Have you ever made your own homemade bagels? If so, kudos to you! The thought of making homemade bagels never even crossed my mind until recently...as in a month ago.I thought the way bagels got their hard, glossy shell was froma really intensive process that normal human beings couldn't replicate. How wrong was I?! Bagels are not hard to make at all and this whole wheat bagel recipe with step-by-step instructions will help you believe that. I make these whole wheat bagels almost weekly now and we love to smear them with my homemade Nutella, classic hummus, or buffalo chickpea salad. If I can do it, you can do it!

Jump To
  • Why You'll Love This Recipe!
  • Ingredients
  • Variations
  • How to Make Whole Wheat Bagels
  • Expert Tips
  • Best Bagel Toppings
  • Recipe FAQs
  • More Whole Wheat Bread Recipes!
  • πŸ“– Recipe

Why You'll Love This Recipe!

  • Going through the steps of this whole wheat bagel recipe will make you feel like a professional bread baker. Seriously, it's so rewarding to make homemade bagels!
  • Like most bread recipes, the list of ingredients is minimal and you probably have most of the ingredients needed for these homemade bagels already.
  • The possibilities are endless when it comes to making bagels. Switch up the dough mix-ins and toppings for a new bagel flavor every week!
  • These homemade whole wheat bagels are delicious plain, toasted, smeared with your favorite spread or used as the bread for bagel sandwiches. They are so helpful to have on hand.
  • Whole wheat bagels freeze beautifully. I love to make a double batch at the start of the week and freeze them pre-sliced so we can enjoy homemade bagels for days!


  • Warm Water - To know your water is at the right temperature, you should be able to place a finger into it without it being too hot. Think bath water! I usually just add some boiling water to tap water until it's warm.
  • Active Dry Yeast - I've never made this recipe with instant yeast. Active dry yeast is always my favorite yeast when making this whole wheat bagel recipe!
  • Whole Wheat Flour - Obviously, you need whole wheat flour when you're making whole wheat bagels. I personally love Bob's Red Mill's whole wheat flour, but any brand should work.
  • Maple Syrup - Maple syrup is my go-to liquid sweetener when making this whole wheat bagel recipe. If you aren't vegan, however, honey should do the trick.

See recipe card below for a full list of ingredients and measurements.


  • Cinnamon Raisin Bagels - Add some cinnamon and raisins to your dough.
  • Everything Bagels - Top your bagels off with onion and garlic granules and seeds after they've boiled.
  • Chocolate Chip Bagels - Add dairy-free chocolate chips to your whole wheat bagel dough!
  • Onion Bagels - Add some finely minced onion or onion granules to your dough and top them off with more onion after boiling.
  • Poppy Seed Bagels - Once your bagels have boiled, sprinkle on some poppy seeds.
  • Sesame Bagels - Top your boiled bagels with white and black sesame seeds for some crunch!
  • Rosemary Salt - Add fresh, minced rosemary to your dough and top your bagels off with flakey sea salt after boiling.
  • Blueberry Bagels - Mix dried blueberries into your bagel dough.

How to Make Whole Wheat Bagels

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Step 1: Pour the yeast mixture into the mixing bowl with the dry ingredients.

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Step 2: Mix on low until most of the loose flour has formed into a dough and it looks somewhat shredded.

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Step 3: Mix on medium for 8-9 minutes until you get a smooth, stiff, elastic dough. Remove the dough from the mixer, form it into a ball and place it in a bowl coated with oil. Cover it with a damp towel and set it in a warm place to rise for about 20 minutes.

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Step 4: Once the dough has risen, cut it into 12 equal pieces.

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Step 6: Pinch the center of each ball of dough to form a hole, gently stretching the hole bigger to form a ring.

Homemade Whole Wheat Bagel Recipe! (7)

Step 7: Boil the bagels 3-4 at a time for 30 seconds on each side. Remove them with a fine-mesh strainer and place on a wire rack to let some of the water drip off.

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Step 8: While the bagels are still wet from boiling, press your desired topping onto the top of the bagels.

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Step 9: Bake the bagels at 425Β°F / 220Β°C for 15 minutes. Then rotate the baking sheets and bake the bagels for about 8-10 more minutes until golden brown on top. Remove the bagels from the oven and let them cool for at least 20 minutes to allow the inside to finish cooking.

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Expert Tips

  1. I used to roll small amounts of bagel dough into a snake and then try to reattach the ends to make a circle. Don't do this! Simple poke a hole in the center of a ball of dough to create the iconic bagel shape. Your bagels will hold together so much better and you won't end up with a seam.
  2. Be sure to press your bagel toppings onto the boiled bagels well. Otherwise all your toppings will fall off.

Best Bagel Toppings

Bagels can be enjoyed just how you would enjoy toast. The toppings and combinations are endless! I'll list out some of my favorite toppings and/or ways to enjoy bagels below:

  • Peanut butter and jelly
  • Chocolate hazelnut spread and banana
  • Hummus and beans
  • Guacamole/avocado bagel
  • Vegan egg and cheese
  • Cream cheese
  • Cinnamon Maple Dairy-Free Cream Cheese
  • Marinara sauce and cheese, melted
  • Savory Vegan Breakfast Sandwich

Recipe FAQs

Are whole wheat bagels really whole wheat?

Oftentimes, store-bought whole wheat bagels also contain white flour or a combination of different flours and are completely whole grain.These homemade whole wheat bagels are made entirely from whole wheat flour!
Yay for fiber, whole grains and protein!

What are different homemade bagel toppings?

One of the best part about bagels is that they can come in so many different flavors and you can create an entirely different flavor of bagel just by switching up the toppings. Some bagel topping ideas are
1. Grated garlic and onion
2. Sesame seeds, poppy seeds and salt (for an everything bagel)
3. Cinnamon and sugar (for a sweet bagel)
4. Rosemary and salt (this is our favorite combo that we get from a local farmers market)
5. Cheese and black pepper
6. Olives
7. Sun-dried tomatoes and Italian herbs

How should I store homemade whole wheat bagels?

Fresh, homemade bagels can get stale pretty quickly. For this reason, I almost always freeze my homemade bagels. Let your homemade bagels cool, then slice them and put them in a freezer-safe zip-lock bag. That way they'll be pre-sliced when you're ready to take them out of the freezer.

How do you reheat a frozen bagel?

How you reheat your bagel will depend on how you stored it. If the bagel has been in the fridge, simply toast the bagel, using the bagel button if your toaster has one If you're pulling a bagel from the freezer, allow it to thaw so you can pull the halves apart. Then select the frozen setting on your toaster and toast the bagel.

What are the best spreads for bagels?

There are so many different spreads you can enjoy on bagels. Some of the post popular or cream cheese, flavored cream cheese, butter, peanut butter, avocado, smoked salmon and egg. You can also use bagels as the bread for your favorite sandwich!

More Whole Wheat Bread Recipes!

  • No Knead Whole Wheat Vegan Sandwich Bread
  • Whole Wheat No-Yeast No-Rise Vegan Pizza Dough
  • Whole Wheat Vegan Cornbread (8 Ingredients!)
  • Easy Whole Wheat Artisan Bread Recipe

πŸ“– Recipe

Homemade Whole Wheat Bagel Recipe! (15)

Homemade Whole Wheat Bagels!

Faith VanderMolen

If you've never made bagels before, I hope this post gives you the confidence you need to give them a go. If I can do it, you can do it!

4.52 from 149 votes

Print Recipe Pin Recipe

Prep Time 1 hour hr 10 minutes mins

Cook Time 25 minutes mins

Total Time 1 hour hr 35 minutes mins



  • Place the warm water and yeast in a bowl and allow the yeast to dissolve completely. Set aside.

  • Combine the flour, syrup, salt and sugar in the bowl of a stand mixer fitted with the dough hook attachment. Pour in the yeast mixture, making sure all of the yeast gets into the mixing bowl.

  • Mix on low until there isn't much loose flour left and a dough looks shredded (about 2 minutes).

  • Increase the speed to medium and continue mixing until you get a smooth, stiff, elastic dough (about 8-9 minutes). If the dough starts separating into 2 sections or gets stuck on the hook, stop the machine and push the dough down to the bottom of the bowl.
    Form the dough into a ball and place it in a large bowl coated with oil. Turn the dough in the bowl so that it gets coated with oil. Cover the bowl with a damp towel and set it in a warm place for it to rise. This will take about 20 minutes. You'll know it's ready when it gets slightly larger and the dough slowly springs back when you press it with your finger. It won't double in size!

  • Preheat your oven to 425 degrees and place a rack in the middle. Fill up a large saucepan with water and bring it to a boil. Once it boils, reduce the heat to medium low so that the water is at a simmer. Cover the pot with a lid until your ready to boil the bagels.

  • Get out 3 baking sheets. Line 2 with parchment paper or a silicone baking mat for baking the bagels and place a wire cooling rack over top of the third. This rack will allow the bagels to drip off excess water after they have been boiled.

  • Turn the dough onto a dry surface and divide it evenly into 12 equal pieces, rolling each piece slightly to form a ball. Keep the dough you're not working with covered with a damp towel so that it doesn't get too dry. Pinch the center of each ball of dough to form a hole, gently stretching the hole bigger to form a ring.

  • Once you have finished forming all of your bagels you are going to boil them 3-4 at a time. Do this by placing 3-4 bagels into the simmering water and let them cook on each side for about 30 seconds. They will sink to the bottom of the pot at first and slowly begin to rise over the course of the minute. Don't forget to flip them over after 30 seconds! Remove the bagels with a fine-mesh strainer. Place the boiled bagels onto the wire drying rack and press your desire topping onto the top of the bagels while they are still wet. Continue this process until all of the bagels have been boiled and garnished with optional toppings.

  • Place the bagels onto the parchment lined baking sheets about 1 inch apart and bake for 15 minutes. Then rotate the pans and continue baking the bagels until they are golden brown on top, about 8-10 more minutes.

  • Remove the bagels from the oven and let them cool on a rack for at least 20 minutes so that the inside can finish cooking.

  • Store in a zip-lock bag for about a week or slice and freeze!*


*You don't want your water to be too hot to touch or else it will kill the yeast.

*To warm up the frozen bagels, simply place them into a toaster straight out of the freezer.


Serving: 1gCalories: 157kcalCarbohydrates: 33gProtein: 6gFat: 1gSaturated Fat: 0.2gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 0.2gSodium: 390mgPotassium: 174mgFiber: 5gSugar: 3gVitamin A: 4IUVitamin C: 0.01mgCalcium: 18mgIron: 1mg

Tried this recipe?Let me know how it was!

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Reader Interactions


  1. K says

    Homemade Whole Wheat Bagel Recipe! (23)
    I am a really amateur baker, but these turned out great for me πŸ™‚ I'm also surprised these taste BETTER than white flour bagels! I'd recommend this recipe to anyone, health conscious or not


    • Faith VanderMolen says

      So so happy to hear that! Thanks so much for sharing!


  2. Kay says

    Hi, was wondering if you can substitute sugar with honey?


    • Faith VanderMolen says

      I think that would work great! Let me know how they turn out for you!

  3. Nan says

    I followed your recipe closely except for halving the amount of salt, and these bagels are the best. Thanks for the terrific recipe.


    • Faith VanderMolen says

      So happy to hear that! Thanks for sharing!


  4. Josephine says

    Hello Faith! I really enjoyed following your recipe, it was easy and simple, and produced some great tasting bagels. However, I only had 9 bagels that were smaller and denser than yours. They weren't tall at all. Do you have any ideas of what went wrong and what I could do to improve it?


    • Faith VanderMolen says

      Hi Josephine! I'm glad you found the recipe simple and the final result tasty. Sorry that they were dense and small though! I'm not sure what happened. It sounds like you followed the recipe exactly? Could your yeast be expired/not fresh? That's my one thought. I hope you have a better result if you try this recipe again!


  5. Jeff Berman says

    These came out amazing! I milled my own flour from hard white wheat berries. I used 1lb berries and cut the water down to 1 1/3 cup, and made 8 bagels instead. I used monk fruit and agave as alternative sweeteners.

    Great recipe!


    • Faith VanderMolen says

      So glad that you liked this recipe and that it worked for you! Thanks for letting me know!


  6. Gail B says

    These are so yummy! Mine came out very puffy, so I think maybe I didn't stretch them enough? I kneaded them by hand, so perhaps that had something to do with it. The taste was delicious. I used sea salt on top, and I can't wait to have them with hummus for breakfast tomorrow. Thank you for the terrific recipe,


    • Faith VanderMolen says

      Sounds like you have a delicious breakfast option now! Thanks for sharing Gail!


  7. Gabby says

    These are so good! I followed the recipe exactly (it's my first time making bagels) and topped mine with sesame seeds πŸ™‚ They are delicious, thanks for the recipe!


    • Faith VanderMolen says

      Oh yay! I'm so glad to hear that Gabby! Thanks so much for sharing!


  8. Trudy says

    I’ve done this recipe a few times and it always works out so well! So easy and delicious.


    • Faith VanderMolen says

      I'm so glad to hear that Trudy! Thanks so much for sharing!


  9. Kanika says

    I tried making half the recipe but the dough was WAY TOO STIFF.. πŸ™
    Did not rise also.. idk what went wrong. Using indian wheat flour


    • Faith VanderMolen says

      I'm not super familiar with indian wheat flour Kanika. I'm sorry they didn't work out for you! Using all whole wheat flour does result in a denser bagel, but sounds like your dough wasn't even usable. Maybe try flour from Bob's Red Mill or King Arther?


  10. Janis says

    So, I have a couple things to say! First off, I didn't use a bread kneader or whatever they're called; just kneaded with my hands, and the bagels turned out great! Also, I used active yeast and, again, turned out great! I will say my bagels did have trouble cooking through evenly, but in the end, not a big deal. I also added some cheese on the top to recreate that asiago-bagel and it was delicious!! I halfed the recipe and with that being said, I only made 6 bagels, but they were still significantly smaller which i assume is due to the rising of the dough. Anyways love the recipe and the fact that it used wheat flour (I used atta)! SO with so many modifactions, the recipe worked out amazing 11/10 would reccomend


    • Faith VanderMolen says

      Thanks so much for sharing Janis! I'm so glad they worked out for you!


  11. Laura says

    Easiest and best bagels I have made!


    • Faith VanderMolen says

      Oh yay! I'm so glad to hear that!


  12. Nada says

    Hello , may I know how many grams in one cup of flour used in this recipe?
    Thank you


    • Faith VanderMolen says

      Hi Nada! Unfortunately I'm not sure. When I google "Whole wheat flour cups to grams" it looks like there is about 120 grams per cup of whole wheat flour so you could start with that!


  13. Jodie says

    I made one hundred percent whole-wheat bagels several years ago and never made them again. I just dug out my recipe and I think I figured out why! I have one of the most complicated ways of making them, lol. With a soaker. A biga. Loads of waiting time. No wonder I never made them again! I'm excited to try your recipe because it's a lot easier πŸ™‚ πŸ™‚


    • Faith VanderMolen says

      I hope you were able to give this recipe a try Jodie! Please let me know how they turn out πŸ™‚


  14. Anon says

    Can you use instant yeast?


    • Faith VanderMolen says

      Hi Anon! I actually haven't tried that so can't say for sure. If you give it a try, please let us all know how it turns out!


    • Cheryl says

      I used instant yeast and they turned out great


      • Faith VanderMolen says

        So great to hear that Cheryl! Thanks for your comment. Enjoy the bagels!

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