Easy Sourdough Bagels with Fresh Milled Flour

These sourdough bagels with fresh milled flour are everything you love in a bagel. They’re chewy, nutty, naturally fermented, and made with real whole grains!

Homemade bagels that taste like real bread? Yes, please. The aroma alone is worth the effort. When I first started milling my own flour, bagels were one of the recipes my kids wanted me to master.

If you’ve never made bagels before, don’t worry. The process is easier than it sounds. Once you do it once or twice, it becomes a cozy kitchen routine. And trust me, pulling a tray of golden homemade bagels out of the oven makes every step worth it.

Looking for more fresh milled flour and sourdough recipes? Our Sourdough Buttermilk Biscuits are always a hit, or you can try making Sourdough Stick Pecan Buns, Sourdough Carrot Cake Focaccia, Sourdough Country Loaf, Sourdough French Bread, or Sourdough English Muffins.

New to baking with freshly milled flour? Take a walk through our Beginner’s Guide or our Grain Guide.

Why You’ll Love Whole Wheat Sourdough Bagels

Freshly milled flour adds a rich, slightly nutty flavor that pairs beautifully with sourdough fermentation. The result? Bagels that are chewy, hearty, and deeply flavorful.

• Naturally Fermented: The sourdough starter gives gentle tang and improves digestibility. No commercial yeast required.
• Chewy Texture: Boiling before baking creates that authentic bagel bite.
• Meal Prep Win: Make a batch and freeze extras for easy breakfasts and lunches. A toasted homemade bagel with cream cheese just feels like a luxury on an ordinary morning!

Sourdough Bagels with Fresh Milled Flour Recipe

Tools

• Grain Mill
• Stand Mixer with Dough Hook Attachment
• Kitchen Scale
• Dough whisk
• Bench scraper
• Plastic Wrap
• Baking Sheets
• Parchment Paper or Silicone Baking Mat
• Large pot (for boiling bagels)
• Slotted spoon
• Kitchen Thermometer
• Cooling Wire Rack

Ingredients

• 115g Sourdough Starter, Active
• 560g Hard White Wheat Berries
• 335g Water
• 20g Honey
• 10g Salt

For the Boiling Bath

• 8 Cups Water
• 1 Tablespoon Brown Sugar
• 1 Tablespoon Baking Soda

Notes:

• The dough is stiffer than a regular bread dough, trust the process!
• I usually start this recipe at 9pm to be able to make bagels in the morning
• Make sure the holes are big enough that baking doesn’t close them up (unless you don’t really mind)
• Boiling bath doesn’t have to be exact, just eye-ball it
• Honey can be subbed for brown sugar in boiling bath
• DON’T skip the boiling, this step is what creates that iconic chewy crust
• Makes 12-13 bagels

Step-by-Step for Fresh Milled Sourdough Bagels

Autolyse: In bowl of stand mixer, whisk together water, sourdough starter, and honey into a slurry. Add fresh milled flour and knead into shaggy dough. Cover and rest 30 minutes.

Knead and Bulk Ferment: Knead in mixer for 5-10 minutes, or until a smooth, stiff dough forms. Bagel dough will feel firmer than typical bread dough because it is lower hydration. Cover and bulk ferment overnight (this can be anywhere between 6-10 hours, depending on house temp).

Divide Dough: Divide the dough into 12-13 equal pieces and roll each piece into a ball. Cover and let dough balls rest 10 minutes.

Shape and Rise the Bagels: Poke a hole in the center with your finger and gently stretch it to form the classic bagel shape. Place shaped bagels on a parchment-lined baking sheet or on a silicone baking mat. Cover and let them rise for 3-6 hours (again depending on house temp) or until puffed.

Boil the Bagels: Near the end of rising, preheat your oven to 425°F, bring a large pot of water to a gentle boil. Add the sugar and baking soda. Boil bagels 3-4 at a time for 45-60 seconds on each side. Remove with a slotted spoon and place back on the baking sheet.

Bake: Bake for 16-20 minutes, or until the bagels are golden brown and the interior temperature is 205 degrees.

Cool: Cool on a rack before slicing and shmearing.