The Best Homemade Sourdough Whole Wheat Bagels
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If you’ve made my classic sourdough bagels before, this whole wheat version is going to feel like a familiar favorite—with a nourishing twist. After so many of you fell in love with that original recipe, I wanted to create a Sourdough Whole Wheat Bagel that brings in extra whole-grain nutrition without sacrificing the chewy bite and soft, pillowy center that makes a bagel truly great.
The process is flexible, too: you can make them in one day or stretch it over two, depending on your schedule. These are not dense or dry in the slightest—just perfectly balanced with a subtle nutty flavor from the whole wheat flour.
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Why You’ll Love This Recipe:
They’re Chewy without being tough
These whole wheat sourdough bagels are satisfyingly chewy. Bread flour and an active sourdough starter give them structure so they hold together when toasted or piled high with cream cheese. If you’ve made Sourdough Bagels or Cinnamon Raisin Bagels before, this dough works just as reliably.
Warm, nutty flavor that comes through
The whole wheat flour adds a natural, nutty taste that makes each bite feel hearty but not heavy. The flavor comes through even when you keep the toppings simple, like just butter or cream cheese.
Works around your day
This dough rises slowly, so you don’t have to spend all day in the kitchen. You can mix it in the morning and bake later, or start it at night and finish the next day. Planning ahead makes these homemade bagels feel real manageable, and you’re getting real sourdough fermentation here.
Golden, shiny crust you can’t wait to bite
The honey in the boil gives these bagels a glossy, golden finish and the classic chewy bite you expect from a regular bagel. The crust bakes perfectly, too. It’s crisp enough to feel satisfying when you bite into it but still soft and tender. When the bagels come out of the oven, they look amazing, smell irresistible, and taste even better, making it hard to wait before digging in. The odds are you won’t make these just once.
Ingredients & Substitutions
* To find precise measurements, scroll to the bottom of this post to find the recipe card*
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours!
- Bread Flour – You technically can use all-purpose flour for these delicious bagels, but I highly suggest making it with bread flour, as it has a higher protein percentage. This allows the dough to rise at great lengths for a more chewy and enjoyable Sourdough Bagel.
- Whole Wheat Flour – I love the King Arthur brand. Their whole wheat flour added a delicious flavor and nutrition to these sourdough bagels.
- Sugar – I used white sugar for a touch of sweetness, but you can use alternate sugars like cane sugar or honey.
- Honey – Adding a little bit of honey to the boil bath gives your Sourdough Bagels the perfect golden brown, chewy crust once they are baked. This can be substituted with brown sugar or maple syrup as well.
- Water – This mixes with the starter and sugar to make a smooth dough. Getting the water right keeps the dough soft but easy to handle for kneading and shaping. It also helps the flours come together evenly.
- Salt –Good sea salt goes in with the flours to boost flavor and strengthen the dough. It helps the bagels hold their shape while baking. It also balances the sweetness from sugar and honey in the boil.
- Optional Toppings – Add seeds, coarse salt, or anything you like right after boiling while the bagels are still damp. Press them gently so they stick and bake evenly. Toppings give the bagels an extra touch of flavor and texture without changing the dough.
Same-Day Schedule
|
Time |
Process |
|---|---|
|
8:00 AM |
Mix the dough |
|
8:30 AM |
Knead the dough |
|
8:30 AM |
Frist Rise |
|
4:30 PM |
Shape and second rise |
|
5:30 PM |
Boil and bake |
Two-Day Schedule
|
Time |
Process |
|---|---|
DAY 1 | |
|
10:00 PM |
Mix the dough |
|
10:30 PM |
Knead the dough |
|
10:30 PM |
First rise |
DAY 2 | |
|
6:30 AM |
Shape and second rise |
|
7:30 AM |
Boil and bake |
How to Make Sourdough Whole Wheat Bagels
- To the bowl of a stand mixer, add the sourdough starter, water and sugar. Mix until smooth.
- To the wet ingredients, add the flours and salt. Mix again on low speed until everything is incorporated, then knead the dough on medium speed for 6-8 minutes. Knead until the sourdough bagel dough is smooth, pulling from the sides of the bowl, and tacky to the touch.
- Remove the dough and place it in a lightly greased bowl. Cover and let it rest for 30 minutes.
- After 30 minutes, knead the dough for 20 seconds or until a smooth dough ball. Knead by pulling and folding the dough toward the center with your palm. Cover again and wait until it doubles in size. At room temperature (70°F), this can take 8-10 hours. If not ready to bake, refrigerate overnight.
- Once the dough has doubled in size, punch it down to remove all of the air bubbles. Then, place the dough on a lightly floured work surface. Using a bench scraper, divide the dough into 8 equal pieces.
- Pull the corners of each piece toward the center, flip, and then roll each piece of dough into a tight, round dough ball.
- Use your thumb to punch a hole in the middle of the dough ball. Stretch the dough ball with both thumbs, then place each bagel on a parchment-lined baking sheet. Repeat with the remaining pieces of dough.
- Cover the baking sheet with a plastic cover and let the dough rest for its second rise. The final proof is complete when the bagels have grown and look puffy.
- Prepare the boil bath in a large pot of water. With the water boiling, add the honey in and stir until dissolved. Start with 2-3 bagels and keep going until you’re done with the remaining bagels, 30 seconds on each side. Drain and place on a wire rack. Top with any toppings, if desired. Press toppings gently so they stick while the bagels are still damp.
- Bake at 425°F for 20–25 min or until golden brown.
- Cool slightly before slicing. Enjoy!
How to Store
Keep leftover whole wheat bagels at room temperature in a sealed bag or airtight container for up to 2 days.
If you want to save some for later, slice them first and pop them in an airtight freezer bag for up to 3 months. And when it’s time to enjoy a bagel, pull it straight from the freezer and toast it for 2–3 minutes or until heated through. The crumb stays chewy and firm, and the crust crisps up just right, so it feels like a fresh bagel every time.
FAQs
This white whole wheat flour recipe works well with an overnight rise in the fridge. You can mix the dough, let it rest, and then cover it in the fridge once it has doubled in size. Cold dough may take longer during the second rise the next day, so plan for extra time. The flavor often deepens with the extra time, making the bagels taste that much richer.
Bread flour has more protein, which helps build strength in the dough. That strength gives the bagels their chewy texture and helps them hold their shape during boiling and baking. All-purpose flour can work, but the bagels may turn out softer and less structured. The recipe was tested with bread flour for the best results, so using it gives the texture and chew you expect.
Boiling is absolutely necessary because it’s what sets the crust and gives bagels the chewy texture we all love them for. Skipping this step turns them into rolls rather than proper bagels. This recipe says to boil bagels for about 30 seconds for each side. It’s a short boil, but it’s enough to get that classic bagel chew and golden color.
You can use brown sugar or maple syrup in the boil bath instead of honey. Cane sugar or honey can replace white sugar in the dough. Results may vary if you change amounts or types beyond those options. The recipe was not tested with other sweeteners, so sticking to these choices gives the most reliable flavor and texture.
Sourdough Whole Wheat Bagels Recipe
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Equipment
- Large Pot
Ingredients
Sourdough Whole Wheat Bagels
- 150 grams active sourdough starter 2/3 cup
- 250 grams water, warm 1 cup + 1 Tablespoon
- 250 grams bread flour 1 3/4 cups
- 250 grams whole wheat flour 1 3/4 cups
- 40 grams sugar 3 Tablespoons
- 11 grams salt 1 1/2 teaspoons
Boil Bath
- 24 grams honey 1 Tablespoon
Instructions
Make Dough
- To the bowl of a stand mixer, add all of the ingredients and mix again on low speed for 5-6 minutes. The dough should be smooth and tacky to the touch.My water was 110 degrees F. The water shouldn't be hotter than 120 degrees F – otherwise this can kill the sourdough starter.150 grams active sourdough starter, 250 grams water, warm, 250 grams bread flour, 40 grams sugar, 11 grams salt, 250 grams whole wheat flour
- Remove the dough and knead until smooth. Do so by folding a portion of the dough towards the center and pressing down with the heel of your hand. Repeat about 20 times, then place it in a lightly greased, straight-edged bowl. Cover and wait until it doubles in size.This took about 8-10 hours in my 70 degree F kitchen. The timing depends greatly on the temperature of your dough and environment. The warmer it is, the faster the dough will rise. The opposite is true for cooler kitchens.
- Once the dough has doubled in size, you can either cover the dough and store it in the fridge overnight or proceed to shaping right away.
- When ready to shape, punch it down to remove all of the air bubbles. Then, place the dough on a clean work surface. Using a bench scraper, divide the dough into 8 equal pieces, about 112 grams each.
- Pull the corners of each piece toward the center, flip, and then roll each piece of dough into a tight, round dough ball. Use your thumb to punch a hole in the middle of the dough ball. Stretch the dough ball with both thumbs about 2 inches, then place each bagel on a baking sheet lined with parchment paper. Repeat with the remaining pieces of dough.
- Cover the baking sheet with this plastic cover and let the dough rest for its second rise. The final proof is complete when the bagels have grown and look puffy.In my 70 degree F kitchen, this took about 1-2 hours with room temperature dough. If the dough is cold from being in the fridge, the second rise took more like 3-4 hours.
- Once the second rise is almost complete, prepare the boil bath. Fill a large pot with about 10 cups of water. Once the water is boiling, add the honey and stir until it is dissolved. Boil 2-3 bagels at a time, 30 seconds on each side. Use a slotted spoon to remove each bagel and place them on a wire rack. Immediately top with any toppings while they are still damp, if desired. Press firmly so the topping adheres to the bagel dough. Repeat with the remaining bagels.24 grams honey
- Once all of the Sourdough Whole Wheat Bagels have been boiled, place them on a parchment paper lined baking sheet. Preheat the oven to 425 degrees F.
- Bake the bagels for 20-25 minutes or until golden brown.
- Cool slightly before slicing. Enjoy!
Notes
Topping Ideas We Keep Coming Back To
- Everything Bagel Seasoning-This is a mix of sesame seeds, garlic flakes, onion flakes, poppy seeds, and a little flaky sea salt.
- Poppy seeds– For crunch. They’re great on their own or mixed in with Everything Seasoning.
- Sesame seeds-Toasty, nutty, and always good-looking after baking. Use white, black, or a mix of both, whatever you have on hand.
- Garlic or onion flakes-Super flavorful, especially if you like a savory bagel with cream cheese or egg.
- Shredded cheese-I love Asiago cheese. I press it into the top and bottom of the bagel so it bakes up extra crispy and golden.
- Cinnamon crunch– This one’s my kid’s favorite, and honestly, I haven’t met a kid who doesn’t love it. I share the recipe & step-by-step process on my Sourdough Pumpkin Bagels recipe.
Ingredients & Substitutions
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours!
- Bread Flour – You technically can use all-purpose flour for these delicious bagels, but I highly suggest making it with bread flour, as it has a higher protein percentage. This allows the dough to rise at great lengths for a more chewy and enjoyable Sourdough Bagel.
- Whole Wheat Flour – I love the King Arthur brand. Their whole wheat flour added a delicious flavor and nutrition to these sourdough bagels.
- Sugar – I used white sugar for a touch of sweetness, but you can use alternate sugars like cane sugar or honey.
Love the nutty flavor that the whole wheat flour brings to these chewy and delicious bagels. Not dense at all and extra nutrition – win, win!
I usually make your sourdough bagels and they are my favorite. I made your whole wheat ones today and they are perfect.
I’m so glad to hear that! I love that you gave the whole wheat version a try and that it lived up to your expectations. Thanks for sharing — happy bagel baking!