These fresh-milled flour sourdough bagels are chewy, hearty, and deeply satisfying in the way all good from-scratch bread should be. Made with whole wheat berries milled fresh at home, they have a sturdy crumb and rich flavor that hold up well to the classic boil-and-bake method.
This is an overnight recipe, which makes it easy to mix the dough before bed and bake the bagels the next day—perfect for a slow, from-scratch breakfast at home.
If you’re looking for other fresh-milled breakfast recipes, you might also enjoy my fresh milled pancakes, waffles, and blueberry muffins.
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Why You’ll Love This Recipe
Recipe Tips
- Expect a firm dough. Bagel dough is much stiffer than sandwich bread or rolls. After kneading, it should be smooth, not sticky, and pull away from the bowl.
- Fresh milled flour absorbs water slowly. If the dough feels dry during mixing, add water a little at a time until it comes together.
- Don’t rush the rise. Whole-grain sourdough moves slower than white flour. Let the dough rise until puffy, not doubled.
- Boil the bagels fully. The full two minutes per side is what gives bagels their chewy crust.
- Bake until deeply golden. Whole-grain bagels benefit from good color for the best flavor and texture.
Ingredients
Bagel Topping Ideas
Once the bagels are boiled and cool enough to handle, dip one side into your favorite toppings before baking.
- Everything bagel seasoning
- Sesame seeds
- Poppy seeds
- Coarse sea salt
- Dehydrated onion or garlic
- Cheddar cheese
- Cinnamon sugar (for a lightly sweet bagel)
You can also leave them plain—freshly milled bagels have plenty of flavor on their own. My favorite way to eat them is slathered with grass-fed butter or topped with cream cheese or homemade ricotta.
How to Make Fresh Milled Flour Sourdough Bagels
1. Mill the Flour
Mill 575 g hard wheat berries on the lowest setting of your grain mill and set aside.
2. Mix the Dough
Add the sourdough starter, water (290 g), salt, and sugar to the bowl of a stand mixer and stir to combine.
Add the freshly milled flour and use a spatula to bring the dough together as best as possible. The dough will be very stiff — that’s normal for bagels.
Change to the dough hook and mix the dough on low speed for 6–7 minutes.
As the dough mixes, add more water, 10 g at a time, as needed. I usually end up adding 20-30 g more water, for a total of 310-320 g water.
(Alternatively, knead by hand for about 10 minutes.)
By the end of kneading, the dough should feel firm and smooth, not sticky, and should pull away from the sides of the bowl while mixing.
3. Overnight Rest
Once mixed, cover the bowl and let it rest at room temperature for 8–12 hours.
I like to make this before bed and let it sit overnight. It should rise to double its size by the next day.
4. Divide & Shape
Turn the dough out onto a clean work surface. Weigh the finished dough, then divide it evenly into 8 pieces to make even bagels.
Shape each piece into a tight ball.
To shape the bagels:
- Place a dough ball in front of you
- Press your thumb straight through the center of the dough to create an opening.
- Gently stretch and shape into a ring
Set the shaped bagels onto a parchment-lined baking sheet, spacing them slightly apart.
Cover the bagels (I like to use plastic wrap) and let them rise until puffy.
This usually takes 60–120 minutes, depending on room temperature. I let mine rise for about 2 hours.
5. Boil the Bagels
Preheat oven to 425°F (218°C). Heat 6 cups of water in a large pot until boiling, then stir in 1 tbsp of sugar.
Once the bagels have risen and are puffy, boil them for 2 minutes per side, working in batches of 3–4 bagels at a time so the pot isn’t crowded.
Remove the bagels with a slotted spoon, then place them back on the parchment paper.
6. Add Toppings (Optional)
Once cool enough to handle, dip one side of each bagel into your desired toppings, then return them to the parchment-lined baking sheet.
7. Bake
Bake at 425°F (218°C) for 20–25 minutes, until golden brown. I take mine out at 20 minutes.
Cool on a wire rack before slicing.
Storage & Freezing
Store baked bagels at room temperature for 2–3 days, in an airtight container.
For longer storage, bagels freeze very well. Once completely cooled, slice the bagels and place them in a freezer-safe bag or container. Freeze for up to 3 months.
To serve, toast straight from frozen—no need to thaw.
FAQ
Whether you enjoy them toasted for breakfast or tucked into the freezer for later, these fresh milled flour sourdough bagels are a simple, satisfying addition to any from-scratch kitchen.
More Fresh Milled Breakfast Recipes
Fresh Milled Flour Sourdough Bagels
Equipment
- Grain mill
- Kitchen scale
- Stand mixer with dough hook (or mix by hand)
- Baking sheet
- Parchment paper
- Plastic wrap (or damp towel)
- Large pot for boiling bagels
- Slotted spoon of mesh strainer
- Wire cooling rack
Ingredients
- 575 g hard wheat berries hard white, hard red, or a blend (I used a 60% hard white / 40% hard red blend — 345 g hard white + 230 g hard red)
- 290 –320 g water about 1 1/4 c, adjust as needed
- 100 g active sourdough starter 1/2 c
- 40 g sugar or honey 2 tbsp
- 10 g salt 2 tsp
For Boiling
- 6 cups water
- 1 tbsp sugar
Instructions
Mill the Flour
- Mill 575 g hard wheat berries on the lowest setting of your grain mill and set aside.
Mix the Dough
- Add the sourdough starter, water (290 g), sugar (or honey), and salt to the bowl of a stand mixer and stir to combine.
- Add the freshly milled flour and use a spatula to bring the dough together as best as possible. The dough will be very stiff — that’s normal for bagels.
- Change to the dough hook and mix the dough on low speed for 6–7 minutes. As the dough mixes, add more water, 10 g at a time, as needed. I usually end up adding 20-30 g more water, for a total of 310-320 g water. By the end of kneading, the dough should feel firm and smooth, not sticky, and should pull away from the sides of the bowl while mixing.
Overnight Rest
- Once mixed, cover the bowl and let it rest at room temperature for 8–12 hours.I like to make this before bed and let it sit overnight. It should rise to double its size by the next day.
Divide & Shape
- Turn the dough out onto a clean work surface. Weigh the finished dough, then divide it evenly into 8 pieces to make even bagels. Shape each piece into a tight ball.To shape the bagels:Place a dough ball in front of you.Press your thumb straight through the center of the dough to create an opening.Gently stretch and shape into a ring.
- Set the shaped bagels onto a parchment-lined baking sheet, spacing them slightly apart.
- Cover the bagels (I like to use plastic wrap) and let them rise until puffy.This usually takes 60–120 minutes, depending on room temperature. I let mine rise for about 2 hours.
Boil the Bagels
- Preheat oven to 425°F (218°C). Heat 6 cups of water in a large pot; once boiling, add 1 tablespoon of sugar.
- Once the bagels have risen and are puffy, boil them for 2 minutes per side, working in batches of 3–4 bagels at a time so the pot isn’t crowded.
- Remove the bagels with a slotted spoon, then place them back on the parchment paper until cool enough to handle.
Add Toppings (Optional)
- Once cool enough to handle, dip one side of each bagel into your desired toppings, then return them to the parchment-lined baking sheet.
Bake
- Bake at 425°F (218°C) for 20–25 minutes, until golden brown. I take mine out at 20 minutes.
- Cool on a wire rack before slicing.
Notes
- Bagel dough should be firm and smooth, not sticky, and should pull away from the bowl after kneading.
- Start with the lower amount of water and add more a little at a time as the dough mixes, just until it comes together.
- Whole-grain sourdough rises more slowly than white flour; look for the dough to become puffy, not doubled.
- Boil the bagels for the full two minutes per side to achieve a chewy crust.
- If you don’t have a stand mixer, you can knead by hand for 10 minutes.
- Store baked bagels at room temperature for 2 to 3 days in an airtight container.
- For longer storage, slice and freeze bagels for up to 3 months.
- Toast directly from frozen to reheat.
