Whole Wheat Sourdough Bagels

Up your sourdough bagel game with these perfectly chewy and puffy 100% whole wheat bagels. They can be topped any way you like and are even better made with fresh milled flour!

Though I enjoy my regular white flour sourdough bagels, whole grains really keep our family full and satisfied for breakfast. And happily, there is nothing dense about these bagels!

I love to share whole grain sourdough recipes on my blog that are actually pleasurable to eat.

Barley malt syrup gives the bagels a traditional flavor, or you have the option to use honey or a combo of both. The bagels are boiled before baking for their signature chewy texture.

After you’re done here, try my Whole Wheat Sourdough English Muffins or my soft 100% Whole Wheat Sourdough Sandwich Bread!

Why Make Whole Grain Bagels?

The sourdough movement has exploded in the past several years with primarily white flour recipes. But whole grain (wholemeal) flour can be successfully used in sourdough baking too!

Flour that has been stone-milled from the entire kernel of grain has so much to offer as far as fiber, nutrition, and flavor. This is because the wheat’s germ, bran, and oils are not removed from the flour.

Milling my own flour at home has really opened up my world in the kitchen.

Fresh milled flour can be compared to grinding your own coffee beans at home verses purchasing pre-ground coffee–the flour is just that much more flavorful and aromatic.

I mill hard red wheat berries (bagels pictured) or hard white for this bagel recipe. You can also use store-bought whole wheat or white wheat flour with great results!

Whole Wheat Sourdough Bagels Baking Schedule

*The strength of your starter, the temperature in your home, and other factors will affect how long each step will take. This timeline is based on a final dough temp of 81°F and a room temp between 76°-78°F. If your dough/home is cooler, expect the dough to move slower.

Feed your starter several hours prior to baking the recipe and allow it to peak.

Approximate timing:

• Mix and rest: 40 minutes
• Bulk fermentation:  3 hours, 40 minutes
• Pre-shape, shape, and proof: 1 hour, 20 minutes
• Boil and Bake: 35 minutes

You have the option to cold retard the dough overnight, if you would like. If you want to do this, refrigerate the dough near the end of bulk fermentation and shape and proof the bagels the next day. They will take longer to proof since the dough is cold.

Tips for Making Whole Wheat Sourdough Bagels

• Use whole wheat starter for 100% whole wheat sourdough bagels. White starter will work as well, or you can make a levain (prepared starter) by feeding some of your white flour starter with whole wheat flour ahead of time.
• The bagels will collapse in the boiling pot or oven if over-proofed. They should feel soft to the touch and look slightly puffy, but don’t push the proof further than that. On the other hand, the bagels should float in the boiling pot. If they sink to the bottom, they have not proofed enough and will bake up small and dense.
• You can easily double the recipe. Just use two half sheet pans and rotate the pans halfway through baking if the bagels aren’t browning evenly.
• I’ll be showing you my preferred shaping method to give the bagels the best structure. During testing, I tried a simpler method of stretching the balls of dough into bagel shapes, but those bagels looked less appealing.
• Proofing is the step to nail for the puffiest bagels! More about this in the step-by-step section.

Whole Wheat Sourdough Bagel Topping Ideas

You can leave these bagels plain or top them however you like! Here are some ideas:

• Sesame seeds
• Poppy seeds
• Everything Bagel Seasoning
• Shredded asiago cheese
• Dehydrated minced onion or garlic

How to Make Whole Wheat Sourdough Bagels (Step-by-Step Instructions)

Step 1 – Mix and Knead Whole Wheat Sourdough Bagel Dough

I like to knead this dough in my Bosch mixer fitted with the dough hook, but you can knead by hand as well.

Into the mixer bowl add all the ingredients together: ripe starter, water, olive oil, barley malt syrup (or honey), kosher salt, and whole wheat flour.

Mix on low speed for a couple minutes until everything is thoroughly combined. Then cover the dough. Allow it to rest for 30 minutes to kickstart gluten development.

After the rest time, begin to knead the dough on the lowest setting you can get away with without the mixer lagging. This dough is on the stiff side, though not as stiff as some bagel recipes.

Knead for about 6 minutes or until the dough passes the “windowpane” test of gluten development. This means the dough will stretch very thin before it tears.

This particular dough won’t be very extensible (stretch far) due to the low hydration, but you should still be able to see that the gluten structure is strong.

Proper kneading insures the finished bagels will rise well with a chewy texture instead of having a shaggy, crumbly texture.

Step 2 – Bulk Fermentation

Dampen your hands and form the dough into a ball. Place the dough in a container for bulk fermentation and press the surface flat.

I like to use a straight-sided Cambro food storage container and mark the starting point of the dough with a dry-erase marker.

Set the dough in a warm spot and allow it to rise to 75% it’s volume. It does not need to double in size.

Step 3 – Preshaping and Final Shaping

Preshaping

Turn your dough out onto your un-floured countertop and divide it into 6 pieces. You can weigh dough and make each bagel 141g if you want them exactly the same size.

Form each piece into a ball. Cover and let them rest for 15 minutes before you shape them.

Final Shaping

For the final shaping, place the first ball smooth-side-down on your counter. Use a very light dusting of flour as needed to prevent sticking.

Press the dough flat with your fingers to pop any air bubbles (degas). Begin rolling the piece up from the top or bottom, cinching the dough into itself as you go. You’ll end up with a short tube.

Roll the tube outwards against the counter with both hands to lengthen it to about 10 inches.

Next, open up and flatten one end of the tube. Bring the opposite end around onto the flat end to form a bagel shape and pinch the flattened dough around the round end to seal.

Finally, place your hand inside the bagel and roll the bagel back and forth a bit on the counter to smooth the seal. Then you’re done! Shape the remaining bagels the same way.

Step 4 – Proof

Line a half sheet pan with parchment paper and sprinkle with a thin layer of cornmeal. Arrange the bagels evenly on the pan and cover them with plastic wrap.

Allow them to proof for about an hour until they look slightly more poofy and feel softer to the touch.

Be careful that they don’t overproof, or they will flatten in the boiling pot or oven.

Meanwhile, preheat your oven to 425°F with a rack set in the center. Set out any toppings you’ll be using.

Prepare your boiling pot by adding tablespoon of barley malt syrup or honey into the pot and bringing it to a gentle boil over medium-high heat.

Step 5 – Boil, Top and Bake

As soon as the bagels are fully proofed, boil three bagels at a time for 1 minute on each side. You should be able to gently lift them off the baking tray with your hands to transfer them into the water.

The bagels should float in the water if they have proofed enough!

Use a slotted spider spoon to lift them out of the pot. Allow the excess water to drain off and then place the bagels back on the prepared baking sheet.

Sprinkle on your toppings of choice while the bagels are still damp.

Finally, bake the bagels for 20-25 minutes or until they are golden in color. Cool them completely on a wire rack before slicing or storing.

We love to toast our bagels before spreading them with cream cheese or butter!

How to Store Whole Wheat Sourdough Bagels

Sourdough bagels will store in an airtight container at room temperature for 2-3 days.

We prefer to slice and freeze any leftover bagels on baking day. Then we toast them from frozen for quick breakfasts later.

I’m so grateful for your comments, reviews, and questions! Your star ratings help others discover my recipes, and your feedback helps me make improvements. Thank you for your support!