Simple Whole Wheat Sourdough Bagels with a deliciously tangy and chewy crust. This bagel recipe is so easy to make (same-day) and is constantly on repeat. Made with wholesome whole wheat flour that is freshly milled and an active and bubbly starter, these are the best sourdough bagels! They are amazing served fresh and taste just as good from the freezer! We love them with savory, homemade everything bagel seasoning!

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Sourdough Bagels are one of my favorite ways to use up sourdough starter! Every few weeks I feed my starter and make this Whole Wheat Sourdough Sandwich Bread, English Muffins, or these delicious bagels!

Whole Wheat Bagels are just as quick to make as regular sourdough bagels only with a few extra steps to make them healthier! Using whole grains is way better than store-bought white flour and comes with many health benefits. Start the morning by fermenting your freshly milled grains to develop the flavors, and make the bagels easier to digest. Then bake them in the evening and you’ll have breakfast or lunch taken care of!

Sourdough Bagels

There is also no yeast or leavening agents in these, we are relying on the active yeast in the starter plus its gut friendly and way healthier! Combined with the freshly milled grains you are making super wholesome food here!

Milling fresh flour will give you a very flavorful, really digestible, and highly nutritious baked good. I use this grain mill to make the flour in seconds and when I do that I know the bran and wheat germ is packed with fiber, full of vitamin B6, folate, thiamin, zinc, magnesium, manganese, and vitamin E.

Not only is it delicious but it’s an easy way to fill up your belly and get the fuel you’ll need for busy mornings! Because whole wheat is rich in fiber you can stay full longer too!

These sourdough bagels are ever so lightly tinted when using a lighter grain like hard white wheat. Whereas hard red will give you more robust and darker bagels.

If bagels seem like an overawe and daunting task, they aren’t. My stand mixer does most of the work and all I have to do is shape it and throw it into boiling water a few minutes before baking, everything else is pretty much hands-off.

My kids love them plain slathered in cream cheese and sweet Strawberry Jam but I love to put on everything bagel seasoning or minced onions for extra delicious flavor and nutrients from the different seeds and toppings.

Below, I will share a few different variations and more bagel sandwich ideas.

Baking with whole grains is a little different. You will need a kitchen scale to weigh the exact amount of flour needed. Since freshly milled whole wheat flour absorbs slower than white flour dough, eyeing it can be off. I typically weigh my grains and run them through my grain mill, how much it mills is exactly how much flour I need for the recipe.

How To Make Sourdough Bagels with Freshly Milled Flour

Bagel dough is very stiff so you will want a stand mixer for the job. Kneading it by hand will be very tiresome. The key to a chewy bagel made with whole wheat flour is to knead it for 25 minutes to properly develop the natural gluten. It should pass the window pane test and the dough should be very pliable.

Make sure you start with an active and bubbly starter. I like to feed mine the night before.
In the morning make the bagel dough. In a stand mixer, with the dough hook attachment, combine all of the dough ingredients (water, flour, salt, honey, and sourdough starter) and knead over low speed (speed 2 in my Kitchen-Aid mixer) for 25 minutes. The dough should be smooth and pliable.
Cover the dough with plastic wrap or beeswax wrap and allow the dough to ferment for 6-8 hours.
After the dough has fermented and risen, transfer it to a large silicone pastry mat and divide it into 8 equal pieces.
Roll the dough into balls and poke a hole in the middle with your finger. Stretch out the hole to widen the bagels.
Allow the dough to rise on a silicone-lined baking sheet for up to 2 hours in a warm spot. It could take even faster depending on how warm it is.
Preheat oven to 425°F and bring a large pot (or Dutch oven) of water (about 12 cups) to a boil. Add the baking soda and sugar.
Drop the bagels into boiling water 4 at a time and boil for 60 seconds on each side. Flip the bagels over using a slotted spoon with holes.
Place the boiled bagels over a silicone-lined baking sheet. Dip into toppings of choice and arrange bagels 2 inches apart over the pan.
Bake for 20-25 minutes or until golden brown.

Add-ins and Ways To Serve Sourdough Whole Wheat Bagels:

Here are yummy ways to eat bagels and creative add-ins to add to the dough before shaping.

When shaping gently knead in dried blueberries, chocolate chips, or cinnamon and raisins.
Some topping ideas include shredded cheddar cheese and jalapenos to make Jalapeno cheddar bagels.
Make your own “everything bagel seasoning” by mixing even amounts of dried onion, dried garlic, poppy seeds, and sesame seeds.
Mix brown sugar and cinnamon and then sprinkle over bagels after they have boiled. Bake as directed for a sweet variety.
Sweeten some cream cheese by adding some vanilla or maple syrup.
Cream cheese and salmon lox make delicious sandwiches. I love to add purple onions!
Use your favorite lunch meat to make delicious sandwiches with greens. Cream cheese, Salami, and arugula salad mix make for a quick sandwich idea. I love bagels with mayonnaise and a fried egg topped with American cheese (so yummy)!

How To Store Whole Wheat Sourdough Bagels

Bagels will last up to a week if stored in an airtight bag. It is best to keep them in the fridge if the temperature is too warm in the house. They also get even better in texture once toasted. Since I do make multiple batches, I will store plenty in the freezer. To freeze bagels, I let them cool completely before stacking them in a plastic bread bag and then freeze about 8 bagels at a time. Frozen bagels can be kept in the freezer for up to 3 months. If you slice them beforehand you can save time later after thawing.

Q&A

Can I Use Store-Bought Whole Wheat Flour?

This sourdough recipe is specifically for freshly milled flour. Store-bought wheat flour is different than freshly milled flour and can yield a different outcome because it has been sitting on the shelf some of the nutrients and oil have been lost. It is also usually made from a hard red wheat variety unless stated. I use hard white wheat that is mild in taste and lighter in color.

Are All Bagels Sourdough?

Sourdough not only helps dough rise but creates an incredibly chewy crust and tangy taste making it stand out from other breads. New York-style bagels typically contain enzymes which is basically, another term for sourdough. You can get away with yeasted dough but the texture will be more like bread and not as chewy.

Why Are Bagels Boiled at First?

Boiling bagels help produce a thicker crust and depending on how much baking soda is used it also helps with browning. I use a tablespoon of baking soda and brown sugar for a medium-brown crust if you prefer darker bagels add more baking soda to your boiling water.

Can I Make Whole Wheat Bagels with Sourdough Discard?

This sourdough bagel recipe works great if your sourdough starter is weak or unfed. Make sourdough discard bagels by simply adding commercial yeast to the bread dough before kneading. Typically, one tablespoon is needed for every 560 grams of flour.

Are Sourdough Bagels Healthy?

This sourdough whole wheat bagel recipe is very nutritious using freshly milled whole grains and sourdough. Sourdough makes grains easier to digest and whole grains when freshly milled come with health benefits too.

Tips for Making Whole Wheat Sourdough Bagels:

Don’t over ferment, if you see any excess liquid coming out of the dough it’s been over-fermenting. Freshly milled flour dough does not do well overnight in the fridge. Not only can it oxidize, but it is a heavier dough that slows down the fermenting process and has to come back to room temp way longer. I find it works best at room temp on the same day.
Freshly mill your own flour by using a grain mill and good quality whole grains. I use hard white wheat for bagels as it results in a lighter bagel. I also buy organic whole grains from Azure Standard.
I use a heavy-duty professional HD stand mixer by KitchenAid which works great for one batch of bagels. Depending on what mixer you use it may need to rest for 10 minutes in between the kneading time so that the mixer doesn’t overheat. Bagel dough is very stiff so if you feel like your mixer is getting hot, stop it and give it a rest before proceeding.
Cover the dough well with a wet tea towel, plastic wrap, or beeswax wrap to prevent skin from forming on the dough and from getting too crusty.
Add the baking soda and brown sugar to the water after it starts boiling. Boil bagels 4 at a time to not overcrowd the pot.
Use a slotted spoon or spider strainer to easily remove and drain the bagels from the water.
Freshly Milled flour recipes need to be kneaded longer than regular dough recipes. The longer kneading time ensures a pliable dough and develops the gluten. Whole wheat flour also absorbs slower into the dough so give the dough time to absorb the liquid.
Mix in different types of grains like spelt, einkorn, or kamut.
This whole wheat sourdough bagel recipe can be made with unfed or discarded starter, simply add 1 Tbsp of dry active yeast to the dough.
Start your dough in the morning to get it baked on the same day.
The longer the fermentation the better it is for you.

More sourdough Recipes:

Whether you need a beginners sourdough bread recipe or a staple sourdough sandwich bread loaf, I got you covered! Here are some of favorite sourdough recipes to make!

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