Name: Sourdough Honey Wheat Bagels
Prep time: 600 min
Cook time: 30 min
Ingredients: 3 cups (400g) all-purpose or bread flour ((or a 50/50 blend)); ¾ cup (100g) whole wheat flour; ½ cup (100g) active sourdough starter; ⅓ cup (120g) raw honey; 1 cup (225g) warm water; 1 ¾ teaspoons (10g) sea salt; Wheat germ (optional) (for garnish); 2 quarts water; 1 tablespoon honey

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There’s something special about making homemade bagels. The process is a true labor of love, but the reward is a chewy, flavorful, golden bagel that’s far better than anything store-bought. These Sourdough Honey Wheat Bagels are a perfect balance of hearty earthy whole wheat, natural sweetness from honey, and a beautifully chewy texture.

Let’s dive into the process so you can make your own bakery-worthy sourdough bagels at home!

Why You’ll Love This Recipe:

Unlike commercial bagels made with yeast, these rely on an overnight sourdough fermentation, which not only enhances the flavor but also makes them easier to digest. The cold ferment develops deep, complex notes, while the honey in the dough and the boiling water bath gives them a gorgeous golden crust.

Tools You’ll Need:

Kitchen scale- For accurate hydration and consistent results.
Stand mixer or large mixing bowl- To mix the dough thoroughly (a dough hook helps with enriched or wet doughs).
Measuring cups and spoons- for measuring smaller ingredients.
Bench scraper- For cleanly dividing and shaping the dough.
Parchment paper (4×4 squares)- To prevent sticking during proofing. To line pan for baking. These precut squares are so convenient linked here https://amzn.to/4mAbWHe
Large pot- For boiling the bagels before baking.
Slotted spoon or spider- To safely remove bagels from boiling water. I love this spider strainer linked here https://amzn.to/4kJqvGT
Baking sheet- To bake the bagels evenly.

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Gather Your Ingredients:

Bread flour (or all-purpose)- High protein for strength and chew. I like to do a 50/50 blend to ensure structure and softness for my dough.
Whole Wheat flour- adds flavor and nutrients to the bagels. If you don’t have this on hand you can substitute for bread or all-purpose flour.
Water- Hydrates the bagel dough. Filtered or tap is fine!
Sourdough starter- Natural leavening for flavor, structure, and health benefits. Make sure starter has been fed and is doubled in size.
Honey- Sweetens the bagel dough and helps give bagel a golden brown finish.
Fine sea salt- Balances flavor and strengthens gluten structure.
Wheat Germ (optional)- for garnish on top of bagels. I like Bob’s Red Mill linked here.

Now let’s bake bagels!

Instructions

Step 1: Mixing Dough

In a large mixing bowl, combine the sourdough starter, bread flour, all-purpose flour, whole wheat flour, honey, salt and warm water. Stir until a shaggy dough forms.

Knead the dough for about 10 minutes, until it becomes smooth and elastic. If using a stand mixer, knead on low speed for 10 minutes. After kneading, transfer the dough to a lightly oiled bowl or container. Cover the dough and let it rest for 30 minutes.

Perform a stretch and fold by gently pulling up one side of the dough, stretching it, and folding it back onto itself. Rotate the bowl and repeat on all four sides.

Step 2: Bulk Fermentation

Cover the dough again and let it rise at room temperature, ideally around 75-78°F, for 8-10 hours. If your house is cold, place dough in oven with light on to create a warmer environment. This long fermentation helps develop flavor and digestibility. Because this dough has lower hydration and contains whole wheat, it won’t rise dramatically, this is normal! It’s better to proof this dough longer than not give it enough time, if you cut it short you may end up with a gummy and dense bagel.

Bagel dough after completing bulk fermentation.

Overnight Fermentation Option: After the first rise, transfer the dough to the refrigerator and let it cold ferment for at least 1 hour to firm up, or up to 12 hours overnight for optimal fermentation.

Step 3: Shaping the Bagels

When ready to shape bagels, remove the dough from the fridge. If you refrigerated dough over 6 hours, let it rest on the counter for 30 minutes to take the chill off before weighing and shaping.

Weigh the dough and divide it into equal portions, about 130g per bagel for a standard size.

Shape each portion into a tight ball by tucking the edges underneath. Let them rest on a greased or floured surface.

Prepare 14 squares of 4×4 parchment paper for shaping. I just folded my parchment into roughly this size and cut it. This dough is stickier so it’s important for you not to skip this step. Line your baking tray with your parchment squares and lightly spray with cooking oil to avoid sticking.

To form the classic bagel shape, poke a hole in the center of each dough ball using your thumb, then gently stretch the hole until it’s about 1.5 inches (4 cm) wide. The hole will shrink slightly as the dough rests.

Shape bagels by poking a hole in the center and stretching the dough-transfer to parchment square

Place each bagel on an individual parchment square to prevent sticking.

Cover with a clean kitchen towel and let them rest for 30 minutes while you prepare the water bath.

Step 4: Boiling and Baking

Preheat your oven to 375°F (190°C).

In a large pot, bring 2 quarts of water to a rolling boil. Stir in 1 tablespoon of honey, this enhances the bagels’ golden color and subtle sweetness.

Using the parchment squares, carefully lower a few bagels into the boiling water. Leave the parchment attached initially and remove it with tongs once the bagels are submerged.

Boil for 3 minutes, flipping halfway through. Because of the whole wheat content, these bagels may not float but continue boiling them for the full time.

Boil bagels 3 minutes then strain from water

Remove the bagels with a slotted spoon, letting the excess water drain off, then place them back on the parchment-lined baking sheet. Sprinkled with a garnish of wheat germ if desired.

Bake for 30 minutes, until golden brown and firm to the touch.

Let the bagels cool completely before slicing, this helps set the crumb for the best texture.

Enjoy your fresh homemade bagels!

Yields 7 bagels

How to Store:

Bagels are best enjoyed same-day, but can be kept at room temperature in an airtight container up to 3 days on the counter. Gently reheat by toasting to enjoy!

Freezer Storage- Freeze bagels (sliced or whole) for up to 2 months. Toast straight from frozen or let thaw at room temp then toast.

Do I have to boil them?

Yes, boiling sets the crust and gives bagels their signature chewy bite.

Can I shape them and refrigerate overnight?

Absolutely. Shape and refrigerate after shaping, then proof, boil and bake the next morning.