Sourdough Bagels with Fresh Milled Flour

There is something incredibly satisfying about pulling a tray of sourdough bagels made with fresh milled flour from the oven. With their perfectly chewy crust, soft interior, and rich sourdough flavor, they’re hard to beat!

This overnight sourdough bagel recipe is one of my favorites because most of the work happens the day before. Simply mix and shape the dough, let it rest in the refrigerator overnight, then boil and bake fresh bagels in the morning. They’re perfect for breakfast sandwiches, toasted with cream cheese, or simply slathered with butter while they’re still warm.

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Why You’ll Love This Recipe

• Made with freshly milled whole wheat flour
• Naturally fermented with sourdough starter
• Easy overnight schedule
• Perfect chewy exterior
• Soft and tender inside
• Freezer friendly

Why Fresh Milled Flour?

Fresh milled flour keeps the entire wheat berry intact, including the bran, germ, and endosperm. This means it delivers naturally occurring fiber, healthy fats, and essential nutrients in every bake. When you mill flour fresh, you preserve B vitamins, vitamin E, iron, zinc, and magnesium that disappear during commercial processing.

By using fresh milled flour, you support digestion, steady energy, and overall wellness — not just empty calories.

I have the NutriMill Classic. I use mine several times a week and have had no issues in over two years. It is a great, affordable grain mill.

Why Use Sourdough?

Sourdough fermentation actively breaks down complex carbohydrates and reduces phytic acid in the grain. This process helps your body absorb minerals more easily and improves digestion. The natural bacteria and wild yeast in sourdough also slow down how quickly your body processes carbohydrates, which supports balanced blood sugar.

Sourdough adds depth of flavor while improving the structure and texture of baked goods. When you combine sourdough with fresh milled flour, the two work together to create baked goods that taste better and feel more nourishing.

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Perfectly chewy on the outside, deliciously soft on the inside!

Sourdough Bagels w/ Fresh Milled Flour Ingredients

Dough

• Active sourdough starter
• Water
• Honey
• Fresh milled flour
• Vital wheat gluten
• Salt

For Boiling

• Water
• Baking soda
• Salt

Egg Wash

• Egg
• Water
• Everything Bagel Seasoning (optional)

Fresh Milled Flour Notes

I recommend using freshly milled hard white wheat for these bagels. It creates a lighter color and milder flavor while still producing a wonderfully chewy texture. If using hard red wheat, expect a heartier flavor and slightly darker crumb. This recipe is written using freshly milled flour measured at 125 grams per cup.

Equipment

• Grain mill
• Kitchen scale
• Stand mixer (optional but helpful)
• Large bowl
• Baking sheet
• Parchment paper
• Large pot or Dutch oven
• Slotted spoon

How to Make Sourdough Bagels with Fresh Milled Flour

1. Mix the Dough

In a large bowl, combine the warm water, active sourdough starter, honey, freshly milled flour, and vital wheat gluten. Mix until no dry flour remains.

Cover and allow the dough to rest for 20–30 minutes.

2. Knead

Add the salt and knead for 8–10 minutes.

The dough will be stiff—that’s exactly what you want for chewy bagels.

Rest the dough for 20-30 minutes.

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Starting with a ball and poking a hole is my favorite method. Alternatively you can also use the rope method for shaping.

3. Shape

Next, divide the dough into 4-ounce portions.

Flatten slightly, poke a hole through the center with your finger, and gently stretch the hole until it reaches about 1-1½ inches wide. The hole will shrink slightly during boiling and baking.

Place each bagel on a parchment-lined baking. I love these sheet pans with lids.

4. Cold Ferment

Cover and refrigerate for at least 6 hours or overnight.

5. Boil

The next morning, remove the bagels from the fridge and uncover. Let it come to room temperature 20-30 minutes while you prep.

Preheat the oven to 400°F.

Bring a large pot of water to a gentle simmer and stir in the baking soda and salt.

Carefully lower the bagels into the water, cooking for 20–30 seconds per side.

Remove with a slotted spoon and return to the baking sheet.

6. Egg Wash

Whisk together the egg and ¼ cup water.

Brush each bagel with the egg wash.

Sprinkle with Everything Bagel seasoning if desired.

7. Bake

Bake for 15–18 minutes, or until deeply golden brown.

Allow the bagels to cool for at least 10 minutes before slicing.

Baker’s Tips

• Don’t skip the cold ferment—it develops flavor and makes the dough much easier to handle.
• Freshly milled hard white wheat gives a lighter flavor, while hard red wheat creates a heartier bagel.
• A stiff dough is normal and creates the classic chewy texture.
• Keep the water at a gentle simmer rather than a rolling boil.
• Don’t over-boil. About 20–30 seconds per side is plenty for a chewy crust.

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Sourdough Bagel Topping Ideas

• Everything Bagel
• Sesame Seeds
• Poppy Seeds
• Garlic & Onion
• Asiago Cheese
• Cinnamon Sugar
• Jalapeño Cheddar
• Plain

Flavor Variations

Mix into the dough:

• Cinnamon Raisin
• Blueberry
• Cheddar Jalapeño
• Parmesan Herb
• Roasted Garlic
• Chocolate Chip
• Cranberry Orange

Storage

Store in an airtight container for up to 3 days.

Freeze sliced bagels for up to 3 months.

Frequently Asked Questions

Why are my bagels chewy?

A stiff dough combined with boiling before baking creates the classic chewy crust that homemade bagels are known for.

Can I use discard?

This recipe works best with an active, bubbly starter for the best rise and texture.

Why boil bagels before baking?

Boiling gelatinizes the outside of the dough, creating the chewy crust and helping the bagels keep their shape.

Can I freeze the dough to bake later?

Yes! Follow steps 1-5, after boiling put the bagels in the freezer. To bake, thaw 20 minutes, then brush with egg wash and bake as normal. It may take a few extra minutes of baking time.

What to Serve with Homemade Bagels

These bagels are delicious with:

• Cream cheese
• Farm fresh eggs
• Bacon or sausage
• Garden fresh tomatoes
• Homemade jam
• Honey butter
• Smoked salmon
• Avocado

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Did You Make This Recipe?

I’d love to hear how it turned out! If you enjoyed this recipe, please leave a ⭐⭐⭐⭐⭐ rating and a comment below. Your reviews not only make my day, but they also help other home bakers find and trust my recipes.

Save this recipe for later on Pinterest so it’s easy to find next time. While you’re there, follow Paradise Acres Homestead for more fresh milled flour recipes, sourdough baking, and from-scratch homestead favorites.

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