Fresh-Milled Sourdough Bagels
The softest, most nutrient dense fresh milled bagels
Bagels have always been one of my ultimate comfort foods, but these fresh-milled bagels take that to the next level. There’s just something about the crispy, golden shell and the soft, chewy inside that’s impossible to resist. Whether topped with something sweet or savory and paired with tangy cream cheese, they’re pure bliss.
However, for a while, I swore off bagels. The long list of ingredients, excessive sugar, and struggles with gluten made them feel like more trouble than they were worth. But everything changed when I switched to using fresh-milled flour for my sourdough. With this change, I discovered how to turn bagels into a nutrient-dense treat—free of unnecessary additives and absolutely worth enjoying.
You can learn more about our journey to fresh-milled grains here.

The combination of sourdough, and fresh-milled flour in these bagels, brings a tangy depth of flavor and an artisanal touch to your kitchen. With the natural leavening power of your sourdough starter and the added nutrients from your whole grains, these bagels are perfect for breakfast, lunch, or a snack. This recipe makes 12 delightfully chewy bagels.
Ingredients:
Dry Ingredients:
- Fresh-milled hard white wheat: 850g (7 cups)
- Vital wheat gluten (optional): 30g (3 tbsp)
- Salt: 15g (2 tsp)
Wet Ingredients:
- Sourdough starter, active and bubbly: 227g (1 cup) (Read here if you’re unsure if your starter is active)
- Water: 560-570g (2 ¼ – 2 ⅓ cups) (more if needed)
- Honey or sugar: 25g (2 tbsp)
Boiling Water Bath:
- Water: Enough to fill a large stock pot ¾ full
- Honey or molasses: 50g (¼ cup)
Optional Toppings:
- Sesame seeds, poppy seeds, everything bagel seasoning, or coarse salt

My favorite part about this recipe is, most ingredients I have on hand all the time, and with just a few minutes I can mix up the dough in the evening, to have a fresh, warm bagel in the morning.
Measuring Fresh Milled Bagel By Weight
I always recommend measuring fresh milled recipes by weight for the most accurate results. This is especially important when working with fresh-milled flour, as the weight can vary significantly depending on the type of grain and how it’s milled. I personally love using this kitchen scale—it’s affordable, compact, and easy to store.
If you’re measuring by cups, be sure to watch the dough closely. If it feels too stiff or starts tearing easily, adjust by adding a bit more water until the consistency is just right.
Fresh Milled Bagel Variations
Vital wheat gluten can be a bit controversial when it comes to fresh-milled recipes. Personally, I find it helpful in certain recipes, like these fresh milled bagels, though I don’t use it in my traditional breads. I order my vital wheat gluten here.
If you prefer to skip it (or if you’re sensitive to it), that’s totally fine! The bagels will still turn out delicious. I make this recipe all the time with no vital wheat gluten, and have great results. Adding vital wheat gluten gives them a light, fluffy consistency, but it’s completely optional depending on your preferences.
Fresh Milled Bagel flour options
For this recipe, I always recommend using hard white wheat as the base, but you can play around with other combinations if you’d like. Hard wheats have a higher protein (gluten) content, which helps create a better rise. I source all my wheat berries from Azure Standard, but if you don’t have an Azure drop nearby, Central Milling is another great option.
My personal favorite blend is 75% hard white wheat and 25% hard red wheat—the flavor combination is fantastic! Feel free to experiment with different ratios to find your perfect mix.
Instructions:
Step 1: Mill Your Flour
Mill about 900 g (7 cups) of wheat berries into flour. This ensures you have enough for the dough and any extra for dusting.

Step 2: Make the Dough
- In the bowl of your stand mixer, combine the sourdough starter, water, and honey. Stir until the starter is dissolved. Use a large mixing bowl for this if you do not have a stand mixer.
- To the wet ingredients, add the vital wheat gluten (if using,) salt and freshly milled flour. I like to add the flour slowly, 1-2 cups at a time.
- Set your mixer to medium-low speed (I use setting 2 on my Bosch Universal mixer) and knead the dough for 10–12 minutes, until it becomes smooth and elastic. The dough should be stiff but smooth. You can knead by hand for this step if you do not have a stand mixer.
Step 3: Bulk Fermentation
Place the dough in a lightly oiled bowl, cover it with a damp towel, and let it ferment at room temperature for 4–6 hours, or until it nearly doubles in size. For a morning bake, prepare the dough in the evening and refrigerate it overnight, covered, for 8–10 hours. Remove the dough from the fridge in the morning and let it come to room temperature before continuing.
Step 4: Shape the Bagels
- Divide the dough into 12 equal pieces, about 130g each.
- Roll each piece into a ball, then poke a hole in the center with your thumb. Stretch the hole to about 2 inches in diameter, as it will shrink during the next rise.
- Place the shaped bagels on a parchment-lined baking sheet, cover them, and let them rise for 30-60 minutes while you prepare the boiling water.

Step 5: Boil the Bagels
- Preheat your oven to 425°F (220°C.)
- Bring a large pot of water to a rolling boil and add honey or molasses.
- Boil each bagel for 2 minutes per side, then transfer them back to the baking sheet.

Step 6: Add Toppings and Bake
- Sprinkle your desired toppings on the bagels immediately after boiling.
- Bake in the preheated oven for 25-30 minutes, or until golden brown.

Tips for Success:
- Active Starter: Ensure your sourdough starter is bubbly and active for the best rise and flavor. If you’re unsure about the stage of your starter, read more here.
- Hydration Flexibility: Adjust water slightly within the range for consistency based on your flour and environment. Too much flour can make for a more dense bagel.
- Recipe adjustments: If you’d like a sweeter dessert bagel, you can add a bit more sweetener.
These sourdough bagels are a testament to the magic of slow fermentation. Whether fresh from the oven or toasted later, they’ll elevate your homemade bread game. Enjoy!


Fresh Milled Sourdough Bagels
Ingredients
- 850 g Fresh-milled hard white wheat (7 cups)
- 30 g Vital wheat gluten (optional) (3 tbsp)
- 2 tsp Salt
- 227 g Sourdough starter, active and bubbly: 1 cup)
- 560-575 Water (2 ¼ – 2 ⅓ cups) (more if needed)
- 25 g Honey or sugar (2 tbsp)
- Water Enough to fill a large pot ¾ full
- Honey or molasses 50g (¼ cup)
- Optional toppings: Sesame seeds poppy seeds, everything bagel seasoning, cinnamon sugar or coarse salt
Instructions
- Mill about 900g (7 cups) of wheat berries into flour
- In the bowl of your stand mixer, combine the sourdough starter, water, and honey. Stir until the starter is dissolved. Use a large mixing bowl for this if you do not have a stand mixer.
- To the wet ingredients, add the vital wheat gluten (if using,) salt and freshly milled flour. I like to add the flour slowly, 1-2 cups at a time.
- Set your mixer to medium-low speed (I use setting 2 on my Bosch Universal mixer) and knead the dough for 10–12 minutes, until it becomes smooth and elastic. The dough will be stiff but smooth. You can knead by hand for this step if you do not have a stand mixer.
- Place the dough in a lightly oiled bowl, cover it with a damp towel, and let it ferment at room temperature for 4–6 hours, or until it nearly doubles in size. For a morning bake, prepare the dough in the evening and refrigerate it overnight, covered, for 8–10 hours. In the morning, let the dough come to room temp before continuing.
- Divide the dough into 12 equal pieces, about 130g each.
- Roll each piece into a ball, then poke a hole in the center with your thumb. Stretch the hole to about 2 inches in diameter, as it will shrink during the next rise.
- Place the shaped bagels on a parchment-lined baking sheet, cover them, and let them rise for 30-60 minutes while you prepare the boiling water.
- Preheat your oven to 425°F (220°C.)
- Bring a large pot of water to a rolling boil and add honey or molasses. Boil each bagel for 2 minutes per side, then transfer them back to the baking sheet.
- Sprinkle your desired toppings on the bagels immediately after boiling. Bake in the preheated oven for 25-30 minutes, or until golden brown.
- Serve warm with the toppings of your choice
If you put in fridge over night, would you let the dough come to room temp or just divide and shape right out of the fridge? Excited to try these out!!
Yes, I would let the dough come to room temp first so you’re able to work with it!
I’ve been making sourdough bagels for a while now but this is the first time I’ve tried with fresh milled flour! They turned out perfect! 🤗 Thank you Samantha!!
So happy to hear that!!
We love these fresh milled bagels!