Freshly Milled Flour Bagels

If you’ve never made bagels at home, you’re in for a treat. Homemade bagels have a chewy crust, soft interior, and incredible flavor that store-bought bagels simply can’t match.

These 100% freshly milled flour bagels bring even more depth of flavor thanks to the natural nuttiness of whole wheat. The traditional bagel method—boiling before baking—creates that classic chewy exterior while keeping the inside tender.

One of the best tricks for amazing bagels is letting the shaped dough rest overnight in the refrigerator. This slow fermentation helps develop flavor and gives freshly milled flour time to fully hydrate, which improves texture and chewiness.

Once you try homemade bagels, they may become a regular part of your weekend baking routine.

Why You’ll Love This Recipe

• Made with 100% freshly milled wheat flour
• Classic chewy bagel texture
• Simple pantry ingredients
• Overnight option for better flavor
• Freezer friendly for easy breakfasts

Equipment Needed

• Grain mill (if milling wheat berries)

• Large mixing bowl

• Stand mixer with dough hook (optional)

• Kitchen scale (helpful but optional)

• Bench scraper

• Large pot for boiling

• Slotted spoon or spider strainer

• Baking sheet

• Parchment paper

• Cooling rack

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  Ingredients

  Bagel Dough

  4 cups freshly milled hard white wheat flour (480 g)
  1 ½ cups warm water (360 g)
  2 teaspoons instant yeast
  1 tablespoon honey or sugar
  1 ½ teaspoons salt

  Boiling Water

  8 cups water
  1 tablespoon honey or brown sugar

  Optional Toppings

  Everything bagel seasoning
  Sesame seeds
  Poppy seeds
  Shredded cheddar cheese

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  How to Make Freshly Milled Flour Bagels

  1. Mix the Dough

  In a large bowl combine:

  • warm water

  • honey

  • yeast

  Let sit for 3–5 minutes until slightly foamy.

  Add the flour and salt and mix until a rough dough forms.

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  2. Rest the Dough

  Allow the dough to rest 10–15 minutes.

  Freshly milled flour absorbs more liquid than white flour, and resting allows the bran to hydrate for better texture.

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  3. Knead the Dough

  Knead for 8–10 minutes until smooth and elastic.

  The dough should feel firm but slightly tacky.

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  4. First Rise

  Place dough in a lightly greased bowl.

  Cover and let rise 45–60 minutes until slightly puffy.

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  5. Shape the Bagels

  Divide dough into 8 equal pieces.

  Roll each piece into a ball, then poke a hole in the center and stretch gently to form the bagel shape.

  Place on a parchment-lined baking sheet.

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  Optional Bakery Trick: Overnight Bagels

  For the best flavor and chewiness, try the overnight method.

  After shaping the bagels:

  1. Cover the baking sheet loosely.

  2. Place in the refrigerator 8–18 hours.

  This slow rest allows the dough to ferment slowly and gives the bran in freshly milled flour time to hydrate, improving the texture.

  The next day, remove the bagels from the refrigerator and let them sit at room temperature for 20–30 minutes before boiling.

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  6. Boil the Bagels

  Preheat oven to 425°F.

  Bring the water and honey to a gentle boil.

  Boil each bagel 30–45 seconds per side.

  This step gives bagels their classic chewy crust.

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  7. Add Toppings

  Place bagels back on the baking sheet and sprinkle with toppings while still damp.

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  8. Bake

  Bake 20–22 minutes until golden brown.

  Cool on a rack before slicing.

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  Cinnamon Raisin Bagel Variation

  To make cinnamon raisin bagels, add:

  ¾ cup raisins (about 120 g)
  1–1½ teaspoons ground cinnamon
  Optional: 1 extra tablespoon honey or 2 tablespoons brown sugar

  Tip:
  Soak raisins in warm water for 10 minutes, then drain before adding to the dough. This keeps them from pulling moisture out of the dough.

  Add cinnamon with the flour and mix raisins in during the final minutes of kneading.

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  Storage Instructions

  Room temperature: store in an airtight container 2 days

  Refrigerator: up to 5 days

  Freezer: slice bagels and freeze up to 3 months

  Toast directly from frozen.

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  Frequently Asked Questions

  What wheat berries work best for bagels?

  Hard white wheat produces a lighter flavor and softer crumb while still providing strong gluten.

  Can I use hard red wheat?

  Yes, but the flavor will be stronger and the bagels slightly darker.

  Why do bagels need to be boiled?

  Boiling gelatinizes the starch on the surface of the dough, creating the chewy crust bagels are known for.

  Why does freshly milled flour need resting time?

  Whole grain flour absorbs more moisture, and resting allows the bran to fully hydrate for better dough texture.

  Can I make bagels ahead of time?

  Yes. The overnight refrigeration method is a great way to prep bagels the day before baking.

  Can I freeze homemade bagels?

   

  Absolutely. Slice them before freezing so they can go straight into the toaster.