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Whole Wheat Sourdough Bagels – Discard or Active Starter

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These whole wheat sourdough bagels are wholesome, chewy, and easy to make. These bagels are fully fermented, but you can use sourdough discard or active starter–whatever you prefer. If you’ve never made bagels before, have no fear! This step-by-step guide will get you through it and on your way to a nutritious & delicious breakfast.

This is a cooling rack of whole wheat sourdough bagels with various toppings next to cream cheese on white backdrop.

My family loves bagels. Back when my husband and I were first married, we used to pick up bagels all the time at our nearby Bruegger’s Bagels. Eventually, that closed down and there wasn’t a decent place to get bagels. (I’m sure some of you will argue that Bruegger’s wasn’t decent either, hah! But hey, it’s all we really had).

Now our local large grocery store sells fresh bagels in their bakery section, but they’re not quite right. They aren’t chewy–they’re more fluffy and soft. Not really what we preferred in a bagel.

Not to mention my standards for the types of grains I eat have increased over time. It was about time we started making our own homemade bagels with whole grains.

This is a cooling rack of whole wheat sourdough bagels with various toppings with cream cheese.

Why You’ll Love This Sourdough Bagel Recipe

These whole grain sourdough bagels are chewy, tender, and absolutely delicious. They’re better than any whole wheat bagel you’ll get at the grocery store, not to mention filled with the benefits of fermentation. They’re also easy to make and will make you feel like a 5-star baker!

Can I use Freshly Milled Flour?

Yes, this recipe is fresh-milled flour friendly! The process detailed here works great with fresh milled grains or with bagged white whole wheat flour. Use whatever type of whole wheat flour you prefer.

Ingredients

To make these chewy, delicious whole wheat sourdough bagels, you need only a few simple ingredients with some optional ingredients as desired:

  • White Whole Wheat Flour – I used 100% whole grain white whole wheat flour milled from my organic hard white wheat berries. But I have also made this recipe with whole white wheat bagged flour from King Arthur.
  • Sourdough Starter – I use unfed cold starter from my refrigerator. You can also use fresh & active starter. This recipe works great either way.
  • Diastatic Malt Powder – This is an optional ingredient that is used primarily to speed fermentation along if you’re making these bagels in the evening before the morning you want to bake them. If you don’t have this ingredient, you can skip it.
  • Honey & Salt for a little flavor in the dough
  • Honey & Baking Soda for boiling the bagels – These ingredients give the bagels their chewy crust.
  • Toppings of choice – The bagels don’t need toppings, but they’re a fun touch. I use Everything but the Bagel seasoning and a cinnamon-sugar topping for my kids in the photos here, but you can mix it up with whatever flavors you’d like! Try poppy seeds, onion flakes, sesame seeds

What is Diastatic Malt Powder?

Diastatic malt powder is made from sprouted grain, usually barley, that adds additional enzymes to your dough to assist in breaking down some of the carbohydrates. It is thought to give a nice golden brown color and lofty rise. In my experience, the effects of diastatic malt powder are fairly minimal and the most noticeable thing I get from it is a faster fermentation period. That is why I say this ingredient is optional.

These are the bowls of ingredients for whole wheat sourdough bagels on a wooden table top.

Sourdough Recipe Timing Tips

  • Start this dough in the early afternoon the day before you’d like to bake the bagels. The dough needs a few rest periods at different points, plus the fermentation period takes a few hours. I would plan for 5-6 hours to get these bagels to a point where you can put them in the refrigerator for a cold-proof/cold retard overnight, then bake them the next day.
  • One thing I love about this recipe is if I get started a little too late in the day, it’s fine! It doesn’t hurt anything to put these in the refrigerator before they’re finished fermenting if you need to get to bed. You can pull them out in the morning and put them in a warm place for a couple of hours to finish the fermenting before boiling & baking. This is such a versatile, convenient recipe!
  • If prepping these bagels quickly is more important to you than fully fermented dough, then it is fine to add a pinch of yeast to the dough as well. The bagels will pass the “float test” more quickly with a bit of commercial yeast added (see step 4 below for more info about the float test).

Instructions

Follow the steps below to make your own whole-wheat homemade sourdough bagels.

This is a kitchen aid mixing bowl with a shaggy bagel dough.

1. Mix Dough & Rest

Add whole wheat flour, sourdough starter, warm water, honey, salt, and diastatic malt powder (if using) to the bowl of a stand mixer. Turn on the mixer and stir on a low speed until just combined. Stop the mixer and cover the bowl with a damp tea towel. Let the shaggy dough rest for 30 minutes before continuing to step 2.

This is a kitchen aid mixing bowl with dough hook kneading dough.

2. Knead & Rest

Knead the bagel dough with a dough hook on a medium-low speed for about 10-15 minutes. This is a stiff dough, so you may need to give your stand mixer a few breaks if the dough gets tough and tight. After the dough is kneaded, turn off the mixer and let the dough sit 15 min to relax before shaping.

This is a sheet pan of shaped bagels rising.

3. Shape

Divide dough into 10 equal pieces and roll the dough balls until smooth. I like to use a food scale for this, but it’s up to you. Pinch a hole in the center of each dough ball and shape into bagels. Place the shaped bagels onto a parchment-lined baking sheet. Shaping the bagels now and letting them ferment in their bagel shape gives us a lot of advantages for timing and a quicker fermentation time.

This is a bowl of water with a floating bagel.

4. Ferment

Cover with plastic wrap and let bagels do their bulk fermentation at room temperature until they can pass the float test. This takes me about 4 hours, but it may go faster if you use active sourdough starter or have a warmer environment. 

To do a float test, place a bagel into a small bowl of water. The bagel should rise to the surface and float. Remove the bagel from the water and gently shake off excess water and put it back on the baking sheet and cover it with plastic wrap. 

At this point, you can skip to step 6 if you want to boil them right away, or you can proceed to step 5 and do a cold-proof overnight to deepen flavor and to have fresh bagels for breakfast.

Sheet pan of rising whole grain sourdough bagels.

5. Cold Proof

Place the covered sheet pan of bagels in the refrigerator to cold-proof overnight.

This is a pot of boiling water with bagels next to a sheet pan of bagel and bowls of toppings.

6. Boil Bagels

The next morning, preheat oven to 400 degrees F. Remove the sheet pan of bagels from the fridge. Put a large pot of water on the stove with 1 tbsp baking soda and 1 tbsp honey added. Bring to a boil. Place 2-3 bagels in the pot at a time and boil for 1-2 minutes per side, (2-4 minutes total) for chewy bagels. Use a slotted spoon or tongs to flip halfway through.

This is a pot of boiling water with bagels next to a sheet pan of bagel and bowls of toppings.

7. Dip in Toppings

If you want to put toppings on your bagels, immediately place the boiled bagels into a small bowl of toppings, then place them back on the baking sheet.

This is a person putting a sheet pan of bagels into the oven.

8. Bake

Bake at 400 degrees F for 20 minutes. Remove from the oven when golden brown and remove bagels from the sheet pan to cool on a wire rack.

Quick Tips

Keep the bagels covered well with plastic wrap when fermenting to prevent them from drying out. A damp kitchen towel could also work.
-The parchment paper may get damp overnight in the fridge from the bagels, but it won’t hurt anything. You can continue to use the parchment paper as long as it’s still in good condition.
-If using tongs to maneuver bagels in the boiling water, be gentle with them to avoid breaking the dough.
-If you use sugar as a bagel topping, keep an eye on it to make sure it doesn’t burn in the oven. Try not to overbake them.
-For best results, eat these bagels the day they were made or plan to freeze some. This is one fresh bread product I find that doesn’t hold up well over multiple days. They are best eaten fresh or frozen once cooled.

Swaps & Variations

This recipe has also been tested with hard red wheat it that can easily be substituted for hard white if you want a more rustic bagel. We have not tested it with other whole grain flours, though.

If you want to try making these with other grains, I recommend keeping at least 80% of the flour (400 grams) a hard red or white wheat. You can add 100 grams of your other favorite grain. If you find a winning grain combination, I’d love to hear about it! Let me know in the comments!

Serving Suggestions

  • I recommend topping these delicious bagels with fresh cream cheese or warm, melty grassfed butter, peanut butter and honey, or make a fresh bagel sandwich with toppings of choice.
  • You can also use these bagels to make freezer breakfast sandwiches with egg, sausage, bacon, and/or cheese. You could make them all at once, wrap in foil, then freeze.
    • Heat them in the oven or air fryer at 350 degrees F for about 30 minutes or until warm all the way through. You can also remove the foil, wrap the sandwich in a damp paper towel, and microwave it for 1-2 minutes. If more time is needed, add 30 seconds at a time.

Nutritional Information

This recipe makes 10 bagels. The nutritional information given below is my best calculation based on my chosen ingredients and process. Nutritional info can vary for many reasons. For more individualized results, calculate the info on your own using a calorie counting app with your chosen ingredients.

For one bagel, the nutritional info is as follows:

  • Calories: 196
  • Protein: 7 gram
  • Fat: 1 gram
  • Carbs: 42 grams
  • Fiber: 6 grams

Recipe Notes

Storage, etc.

This is a cooling rack of whole wheat sourdough bagels with various toppings next to cream cheese bowl with a knife.

Other Sourdough Bread Recipes

Want some other whole wheat sourdough recipes?

Try my 100% whole wheat fluffy sourdough bread, my 100% red wheat sourdough loaf, and my cranberry-orange sourdough!

100% whole wheat sourdough slices on cutting board
cranberry sourdough bread sliced in half

FAQ

Are sourdough bagels healthy?

Whole wheat sourdough bagels are made from nutritious whole grains for added fiber and nutrients. The term “healthy” is subjective and varies from person to person, but if you enjoy eating bread and grain products, whole wheat sourdough bagels are a wholesome addition to your diet.

Is whole wheat good for sourdough?

Yes, whole wheat is great for sourdough! Remember that up until the late 1800s, white or sifted flour was not a common food product in most households. Sourdough has been around since at least 3000 BC, made with a variety of wheat and other grains grown by many cultures throughout history. When people say you can’t make sourdough with whole wheat, it’s really that they aren’t sure how to do it because you absolutely can and people have been doing it longer than they have been with white flour.

Are bagels more unhealthy than bread?

Bagels and bread are made from virtually the same ingredients. On a gram-per-gram basis, the nutrition is similar.

You’ll Love this Easy Whole Grain Sourdough Bagels Recipe!

Give this recipe a try and let me know how it goes! Please leave a comment and review! It means the world!

This is a cooling rack of whole grain sourdough bagels with various toppings next to cream cheese bowl with a knife.
Print Recipe
5 from 1 vote

Whole Wheat Sourdough Bagels – With Discard or Active Starter

These chewy, hearty, and delicious whole wheat sourdough bagels are easier to make than you think! This recipe is a nutritious way to enjoy your favorite bakery treat.
Prep Time1 hour
Cook Time20 minutes
Fermentation Time + Overnight Fridge Time12 hours
Total Time13 hours 20 minutes
Course: Breakfast, Snack
Cuisine: American
Keyword: 100% whole wheat sourdough bread, fresh milled flour sourdough bagels, sourdough bagels, whole wheat bagels
Servings: 10 bagels
Calories: 191kcal
Author: Holly Lee
Cost: $5

Equipment

Ingredients

Bagel Dough

  • 500 grams white whole wheat flour (hard white wheat)
  • 100 grams sourdough starter discard works well, active is also fine
  • 300 grams warm water
  • 30 grams honey
  • 10 grams salt
  • 7 grams diastatic malt powder (optional)

For Boiling

  • large pot of water
  • 1 tbsp baking soda
  • 1 tbsp honey
  • optional toppings–Everything but the Bagel seasoning, poppy seeds, cinnamon sugar, etc.

Instructions

  • Add whole wheat flour, sourdough starter, warm water, honey, salt, and diastatic malt powder (if using) to a mixer bowl. Turn on the mixer and stir until just combined. Stop the mixer and cover the bowl with a damp tea towel. Let the shaggy dough rest for 30 minutes before continuing to step 2.
  • Knead the dough with a dough hook for about 10-15 minutes. This is a stiff dough, so you may need to give your stand mixer a few breaks if the dough gets tough and tight. After the dough is kneaded, turn off the mixer and let the dough sit 15 min to relax before shaping.
  • Divide dough into 10 equal size balls and roll them smooth. I like to use a food scale for this, but it's up to you. Pinch a hole in the center of each dough ball and shape into bagels. Place onto a parchment-lined baking sheet and cover the shaped bagels with plastic wrap.
  • Let bagels ferment until they pass the float test–this is usually around 4 hours for me, but could be more or less depending on your starter and room temperature. To do the float test, place a bagel into a small bowl of water. The bagel should rise to the surface and float. If it sinks, it needs more time to ferment. Gently shake to remove excess water and place bagel back on the baking sheet.
  • Place the covered sheet pan of bagels in the refrigerator to do a cold proof overnight. See notes for a tip if your fermentation is taking longer than expected.
  • In the morning, preheat oven to 400 degrees F. Remove the sheet pan of bagels from the fridge. Fill a large pot with water, 1 tbsp baking soda, and 1 tbsp honey. bring to a boil. Place 2-3 bagels in the pot at a time and boil for 1-2 minutes per side, (2-4 minutes total), using a spoon or tongs to flip halfway through.
  • If you want to put toppings on your bagels, immediately place the wet bagel from the boiling water pot into a small bowl of toppings, then place on the baking sheet.
  • Bake at 400 degrees F for 20 minutes. Remove from the oven when golden brown.

Video

Notes

I recommend starting this dough in the early afternoon the day before you’d like to bake the bagels.
If the bagels aren’t done fermenting but you’d like to go to sleep, place the sheet pan (covered in plastic wrap) in the refrigerator. Take it out in the morning and put in a warm place to finish fermenting, then boil them once they pass the “float test.”

Nutrition

Calories: 191kcal | Carbohydrates: 41g | Protein: 7g | Fat: 1g | Sodium: 718mg | Potassium: 58mg | Fiber: 5g | Sugar: 4g | Vitamin C: 0.03mg | Calcium: 35mg | Iron: 1mg

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One Comment

  1. 5 stars
    These were so good! The dough is a little stiff, definitely important to keep the dough covered while it rises I learned. But they turned out wonderfully and I’m excited to make them again.

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