How to Make Sourdough Bagels: A Gut-Friendly Classic with a Chewy Twist

If you’ve ever bitten into a chewy, golden bagel and thought, "What if this could be even better?" - the answer might just be sourdough. This post guides you to making the best sourdough bagels at home using your natural starter. Whether you're new to baking or already comfortable with sourdough bread, this recipe transforms that bubbly jar of starter into something delightfully chewy, flavorful, and gut-friendly.

Why Make Bagels with Sourdough?

Let’s be honest - we love sourdough. The flavor is richer, the crust has that perfect bite, and most importantly, it’s better for your gut. Using wild yeast and long fermentation instead of commercial yeast can help make baked goods easier to digest and more nutritious.

According to Harvard Health, fermented foods like sourdough can support a healthy gut microbiome thanks to the natural probiotics they contain. Combining fermented foods with fiber - as in these whole wheat sourdough bagels - can be a win-win for digestive health (Harvard Health article).

If you want to know more about the good benefits of sourdough, check out our post about it!

A Brief History of the Bagel

The bagel originates from Jewish communities in 17th-century Poland, where it was prized for its chewy texture and satisfying crust. When immigrants brought bagels to New York, they quickly became a deli staple. Traditional bagels are boiled before baking - a process that gives them their signature texture.

What makes sourdough bagels special? They replace commercial yeast with natural fermentation, giving them a tangier flavor, better keeping quality, and potential health benefits.

Ingredients for Homemade Sourdough Bagels

This recipe yields about 10–12 bagels.

Dough:

• 650 g bread flour

• 150 g whole wheat flour (optional for flavor and texture)

• 40 g honey or sugar

• 200 g active sourdough starter

• 490 g warm water (35–38°C / 95–100°F)

• 20-30 g salt (as you prefer, for me it is 30)

Boiling mixture:

• 3 L water

• 45 g salt

• 75 g honey

Note: You can substitute more bread flour if you prefer to skip whole wheat. I find it adds both flavor and structure.

Also if you need some help How to Feed Your Sourdough Starter for Perfect Baking Results check out our post!

Step-by-Step Instructions

Feed Your Starter the Night Before

Start with a well-fed, active sourdough starter in peek condition. Feed it the night before baking and allow it to become bubbly and double in size. If you’re unsure how to prepare your starter for baking, read this guide first: How to Feed Your Sourdough Starter for Perfect Baking Results.

Mix the Dough

Combine all dough ingredients in a large bowl and mix until a rough dough forms. Knead for 8–10 minutes by hand (or use a stand mixer) until the dough is smooth and elastic. Cover and let it rest for 1 hour.

Stretch and Fold

To develop gluten and strengthen the dough, do 2–3 sets of stretch and folds at 60-minute intervals. How to? Check out our post about it: Folding Dough: Why It Matters and How to Do It Right.

Divide and Shape the Bagels

Cut the dough into 125–130 g pieces. Shape each piece into a tight ball using a pull-and-tuck method. Then, using a damp finger, poke a hole in the center and gently stretch it into a ring, being careful not to deflate the dough.

Place on lightly oiled parchment paper to prevent sticking. Trust me - don’t skip the oil!

5. Proof the Bagels

Cover the shaped bagels with plastic wrap or a damp cloth and allow them to proof for 3–5 hours at room temperature. In cooler kitchens, you can leave them overnight. The longer the proof, the tangier the flavor.

6. Boil and Bake

Bring water to a boil with honey and salt. Boil each bagel for 1–2 minutes, flipping halfway. The longer the boil, the chewier the texture.

Optional: Brush with egg wash and sprinkle with seeds -sesame, poppy, sunflower, or pumpkin.

Bake in a preheated oven at 220°C (425°F) for 20–25 minutes until golden brown. Adjust timing as needed - every oven behaves a bit differently.

Customize Your Sourdough Bagels

Once you’ve nailed the base recipe, it’s easy to explore fun variations:

• Blueberry sourdough bagels

• Cinnamon raisin sourdough bagels

• Sourdough everything bagels

• Sourdough bagels with discard (great for reducing waste!)

• Vegan sourdough bagels (skip the egg wash)

FAQ: Sourdough Bagels

Are bagels sourdough?

Not usually - traditional bagels are made with commercial yeast. But sourdough versions are naturally fermented, which may offer better flavor and digestibility.

Can I make bagels with sourdough discard?

Yes! It gives you a stronger flavor and is a great way to reduce waste. It might need a bit more time to proof, but in the end, it'll be just as good!

How long do sourdough bagels stay fresh?

Store in an airtight container for 2–3 days or freeze for longer. Toast or drop it back into the oven before serving to refresh the texture.

Are sourdough bagels healthier?

They can be! Thanks to natural fermentation, they may be easier to digest and richer in nutrients. Plus, when made with whole wheat, they offer a bit more fiber - another digestive bonus.

Harvard Health and this article break down why that combo works so well for your body.

Final Thoughts

If you're a sourdough enthusiast, these homemade bagels are a must-try. They're the perfect blend of tradition, flavor, and wellness - whether you're feeding a crowd or meal-prepping for the week.

Ready to bake? Let your starter shine - and if you do try it, I’d love to hear how it goes.

Happy baking & bold bageling! 🥯💛

Other posts you might like:

How to Make a Sourdough Starter from Scratch: A Foolproof Guide

How to Make Homemade Sourdough Bread: A Beginner’s Guide

Folding Dough: Why It Matters and How to Do It Right

How to Feed Your Sourdough Starter for Perfect Baking Results

How to Feed, Maintain, and Strengthen Your Sourdough Start