Sourdough Chocolate Chip Bagel Recipe

Last Updated on October 1, 2025 by Jamie Saechao

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These easy sourdough chocolate chip bagels are bursting with chocolate chips and loaded with flavor.

I have gone through many versions of this sourdough bagel recipe, but none of them gave me that rich chocolate flavor I craved. After all, if you are going to have a chocolate bagel, it may as well be super chocolately right?

I finally hit the jackpot when I modified my double chocolate chip sourdough bread recipe into bagels. Finally, sourdough chocolate bagels with massive amounts of chocolate chips and tons of cocoa flavor!

For more bagel recipes try my classic sourdough bagels and whole wheat sourdough bagels.

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Ingredients

• Fed, active sourdough starter (learn how to maintain yours here)
• Cocoa powder
• All purpose flour
• Brown sugar (light or dark will work)
• Filtered water
• Miniature chocolate chips
• Salt

Recipe Tips

• Bagel dough is always very stiff and dry. Trust the process, by the time you are done kneading the dough it will form into a smooth ball.
• I always knead this dough by hand, but a stand mixer with dough hook can be used as well.
• For fluffy bagels make sure the first and second ferment is long enough.
• Use a kitchen scale for accurate results!
• This recipe is using a kitchen temperature of 70 degrees F. If your kitchen is warmer, bulk fermentation will take less time.
• Some of the chocolate chips on the outside of the dough will melt when boiling, this is normal!
• These bagels often “close up” while baking, and may not have that classic bagel hole.

Timeline

• I like to start this recipe in the evening, around 9-10 pm, and then continue the second ferment the following morning at 7 or 8 am.
• To make this bagel recipe in one day, feed your starter the night before, and mix up your dough around 6 or 7 am to allow for the long ferment. Increase the temperature of your kitchen for a faster ferment.

How To Make Chocolate Chip Sourdough Bagels

Feed your starter 4-8 hours prior to starting this recipe (temperature dependent).

Mix together active starter and water and mix well with a dough whisk or spatula. Add in the flour, salt, cocoa powder, brown sugar, and miniature chocolate chips.

Mix well until all ingredients are incorporated. The dough will be very dry and very stiff. Cover and let rest for 30 minutes.

Knead the dough for 6-8 minutes or until the dough forms a smooth elastic bowl. Cover and allow the dough to bulk ferment for 10-12 hours at 70 degrees F, or until doubled in size.

Line a baking sheet with parchment paper. Dump the dough onto the counter and divide it into 8 equal portions. (I like to use my scale to divide up the dough equally).

Shape each bagel by rolling it in a circular motion to create tension. Then, stick your thumb in the middle of the dough and stretch it outwards to create the hole in the bagel.

Cover the bagels with saran wrap for 30-40 minutes or until visibly puffy.

Preheat your oven, then fill a large pot with water and bring it to a boil. Place each bagel in the boiling water for 30 seconds, then flip each bagle and boil for 30 seconds on the other side.

Place the bagels back on the baking sheet and bake for 25-30 minutes or until no longer doughy.

Why Didn’t My Sourdough Bagels Rise?

Sourdough bagels may not rise as quickly as expected for a few reasons:

• Temperature: If your environment is cold, it will take longer for the bagels to rise.
• Starter: If your starter is very young, it may not be ready yet for recipes like bagels or bread. Make sure you use a well-established starter and add it to the bagel dough at it’s peak activity or just after.

Storage

Store in an airtight container for 4-5 days on your countertop.

To freeze, slice each bagel in half and wrap them individually. Then place in a freezer safe, airtight container for up to 3 months.

Variations

• For a more mild flavor, leave out the cocoa powder!
• 2 tablespoons honey may be substituted for the brown sugar.

More sourdough chocolate recipes:

• Sourdough chocolate cake
• Sourdough chocolate focaccia
• Sourdough chocolate chip pumpkin bread
• Sourdough chocolate croissant loaf