Naturally Fermented Sourdough Bagels with Heritage Flour
If you asked me what my favorite foods were growing up, bagels would definitely be up there. On weekends, my family would pick up fresh bagels, and I’d pile mine high with cream cheese. I never would’ve thought years later I’d be making my own from scratch.
Not to say all store-bought bagels are this way, but many are made with enriched, bleached flour, preservatives, and bioengineered ingredients. And if you have a local bakery that makes them fresh the traditional way, support them! But if you want to make them at home, this recipe is such a good place to start.
I made these sourdough bagels using organic heritage bread flour from Sunrise Flour Mill. It’s milled from pre-1950s wheat varieties, before modern hybridization, which gives it a deeper flavor and makes it easier for many people to digest. It’s freshly milled, more nutrient-dense, and perfect for sourdough. If you’re going to take the time to make bagels from scratch, starting with really good flour makes all the difference.
One of the reasons I love making bagels this way is the fermentation. A true sourdough process gives the dough time to slowly ferment, which helps break down some of the gluten and phytic acid naturally present in grains. That slower rise not only develops better flavor and texture, but many people find it gentler on digestion compared to quick-rise commercial yeast breads.
Ingredient highlight
Heritage Flour from Sunrise Flour Mill
For these bagels, I used organic heritage bread flour from Sunrise Flour Mill.
What makes this mill unique is their commitment to preserving older wheat varieties and milling them fresh without bleaching or bromating. Their flour is never enriched or stripped and then “added back” with synthetic vitamins; it’s simply whole, traditionally grown wheat that’s carefully stone-milled for optimal texture and performance.
Because the grain hasn’t been hybridized the same way modern wheat has, the flavor is noticeably richer and more complex. It performs beautifully in long-fermented sourdough recipes, creating that chewy structure you want in a bagel without feeling overly dense.
If you want to try their flour, my link gets you 20% off!
How I love to eat them
I love eating these sourdough bagels just as they are, toasted with a thick layer of butter or cream cheese. But my favorite way to use them? Breakfast sandwiches.
They’re sturdy enough to hold eggs, cheese, and sausage without falling apart, and the chewy sourdough texture makes them so much better than anything store-bought. If you want the full recipe for how I build mine, I shared it in a separate post here:
Bagel Flavor Varieties
- Jalapeño cheddar
- Caramelized onion & gouda
- Cinnamon raisin
- Chocolate chip
- Everything bagel seasoning
Naturally Fermented Sourdough Bagels with Heritage Flour
Ingredients
- 300 g water
- 125 g active sourdough starter
- 20 g raw honey
- 10 g salt
- 500 g heritage bread flour
- 1 egg whisked (for egg wash)
- Everything bagel seasoning
Instructions
Mix the Dough
- In a stand mixer fitted with a dough hook (or a large bowl), combine water, active sourdough starter, honey, and salt. Add the bread flour and mix until a smooth dough forms.
Bulk Fermentation
- Cover and let the dough rise at room temperature until doubled in size. During this time, perform 2–3 sets of stretch and folds to strengthen the dough.
Cold Ferment
- Refrigerate the dough for a few hours or overnight for deeper flavor and easier shaping.
Shape the Bagels
- Divide the dough into 6 equal pieces (about 160g each). Roll each piece into a ball, then poke a hole through the center and gently stretch to form a ring.
Second Rise
- Let the shaped bagels rise at room temperature until fluffy and slightly puffy, about 1–2 hours.
Boil
- Bring a large pot of water to a boil. Boil each bagel for 1 minute per side. Remove with a slotted spoon and place on a lined baking sheet.
Egg Wash & Season
- Brush the tops with whisked egg and sprinkle generously with everything bagel seasoning.
Bake
- Bake at 425°F for 25 minutes, or until golden brown.
Cool
- Cool completely on a wire rack before slicing.
Notes
- Make sure your sourdough starter is active and bubbly before mixing the dough.
- For extra chew, you can add 1 tablespoon of honey or baking soda to the boiling water.
- Bagels freeze well — slice before freezing for easy toasting.
- Longer cold fermentation will deepen the flavor.
