Sourdough Chocolate Chip Bagels (Same-Day or Overnight)
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If you’ve made (and loved) my classic sourdough bagels, this chocolate chip version is going to feel like a fun little treat you didn’t know you needed. These sourdough chocolate chip bagels are made with 100% sourdough, giving you that same chewy exterior and soft, pillowy interior—just with little bursts of melty chocolate tucked into every bite.
They’re lightly sweet without being dessert-level sweet, making them perfect for breakfast or an afternoon pick-me-up. I love slathering mine with cream cheese, but if you ask me, enjoying one warm straight from the oven is absolutely non-negotiable. You can bake them the same day or let the dough rest overnight for an easy, fresh-baked morning—either way, they’re cozy, nostalgic, and incredibly satisfying.
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Why You’ll Love This Recipe:
Chewy Bagels with a Thin, Slightly Firm Crust
These bagels are soft and tender on the inside, with a thin crust that gives just a bit of bite. Boiling before baking creates the classic bagel texture, firm enough to hold its shape but never hard, while keeping the interior chewy. If you enjoy classic sourdough chew, these are similar to my True Sourdough Bagels or Sourdough Blueberry Bagels. You could also try making a chocolate chip sourdough bread to enjoy the same flavors in a loaf form.
Flexible Timing That Works With Your Plans
You can bake the bagels the same day if your schedule allows, or let the dough rest in the fridge overnight to wake up to warm, fresh bagels in the morning. The slower, cooler rise builds extra depth of flavor and gives the dough a tender, chewy texture. I use this same approach with my Sourdough Cinnamon Raisin Bagels to get consistently structured, perfectly chewy bagels every time.
Delicious and Chocolatey Homemade Bagels
Chocolate chips fold into the dough and soften in the oven without losing their shape. Little pockets of chocolate stay soft and complement the mild tang of the sourdough. It’s the same way in my Sourdough Discard Chocolate Chip Cookies, where the chocolate blends right into the dough.
Ingredients & Substitutions
* To find precise measurements, scroll to the bottom of this post to find the recipe card*
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy sourdough chocolate bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours. Instead of an active sourdough starter, I used discard, and I must say there was a slight difference in flavor.
- Bread Flour – You can use all-purpose flour for these homemade bagels, but bread flour is recommended for its higher protein content. Plus, the bagels come out with a chewier texture.
- Chocolate Chips – I used semi-sweet chocolate chips, but you can use your favorite chocolate like dark chocolate, milk chocolate, or white chocolate chips. For smaller pops of chocolate, use mini chocolate chips. There are plenty of options for you, chocolate lovers!
- Sugar – I used white sugar for a touch of sweetness, but you can use alternatives like cane sugar or honey.
- Honey – Adding a little bit of honey to the boil bath gives your chocolate chip sourdough bagels the perfect golden brown, chewy crust once they are baked. Honey can be substituted with brown sugar or maple syrup as well.
Baking Schedule #1
|
Time |
Process |
|---|---|
|
8:00 AM |
Mix dough |
|
8:30 AM |
Knead dough |
|
8:30 AM |
First dough rise |
|
4:30 PM |
Shaping and second rise |
|
5:30 PM |
Boil and bake |
Baking Schedule #2
|
Time |
Process |
|---|---|
|
DAY 1 | |
|
10:00 PM |
Mix dough |
|
10:30 PM |
Knead dough |
|
10:30 PM |
First rise |
|
DAY 2 | |
|
6:30 AM |
Shaping and second Rise |
|
7:30 AM |
Boil and bake |
How to Make Sourdough Chocolate Chip Bagels
- To the bowl of your stand mixer, add the sourdough starter, water and sugar. Mix until smooth.
- To the wet ingredients, add the dry ingredients, flour and salt. Mix again on low speed until everything is incorporated, then knead the dough with a dough hook on medium speed for about 5-6minutes, until the dough is smooth, pulls away from the sides of the bowl, and feels tacky to the touch.
- Remove the dough and place it in a lightly greased bowl. Cover and let the bagel dough rise for 30 minutes.
- After 30 minutes, pour the chocolate chips on top of the dough and knead for 20 seconds or until a smooth dough ball forms. Use a stretch-and-fold motion, pulling the dough up and folding it toward the center, pressing down with your palm. Cover again and wait until it doubles in size.
- Once the sourdough bagel dough has doubled in size, punch it down to remove all of the air bubbles. Then, place the dough on a lightly floured work surface.
- Using a bench scraper, divide the dough into 8 equal pieces, about 130 grams each.
- Pull the corners of each piece toward the center, flip, and then roll each piece of dough into a tight, round dough ball. Chocolate chips may pop out and this is normal. Use your thumb to punch a hole in the middle of the dough ball. Stretch the dough ball with both thumbs to about 2 inches wide, then place each bagel on a parchment-lined baking sheet. Repeat with the remaining pieces of dough.
- Cover the baking sheet with this plastic cover and let the dough rest for its second rise.
- The final proof is complete when the bagels have grown and look puffy. At 70°F, this usually takes 1–2 hours, or 3–4 hours if the dough is cold from the fridge.
- Prepare the boil bath. Bring a large pot of water to a boil, add honey, and stir until dissolved. Boil 2–3 bagels at a time, 30 seconds on each side. Remove with a slotted spoon and place on a wire rack.
- Bake at 425°F for 20–25 minutes or until golden brown and the internal temperature reaches 200–210°F.
- Cool slightly before slicing. Enjoy!
How to Store
These sourdough chocolate chip bagels are best enjoyed the day they’re baked, but you can definitely store them if needed. Store them in an airtight container at room temperature for up to 2 days.
For longer storage, slice them and pop them in a zip-top bag in the freezer for up to a month. Toast or warm them in the oven to bring back that tender, chewy inside and lightly firm crust.
FAQs
Absolutely! You can leave them out or use other mix-ins like raisins or cinnamon sugar. Refer to my original Sourdough Bagel recipe!
Boiling gives the bagels their classic chew and sets the crust. It helps them hold their shape in the oven and creates a thin, slightly firm exterior while keeping the inside soft and tender.
Yes, all-purpose flour will work, but bread flour gives the bagels more chew and helps them hold their shape. Using all-purpose may make them a bit softer and less chewy, but they’ll still taste great.
Yes, technically you can use sourdough discard, but the rise will take longer. This recipe is specifically tested to use an active and bubbly starter. If you want to use discard, then I would use my Sourdough Discard Bagel recipe! It uses sourdough discard and instant yeast and is ready to bake in just 2 hours. You can knead in chocolate chips after a short rest period, just like this recipe.
Sourdough Chocolate Chip Bagels Recipe
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Equipment
- Large Pot
Ingredients
Sourdough Whole Wheat Bagels
- 150 grams active sourdough starter 2/3 cup
- 250 grams water, warm 1 cup + 1 Tablespoon
- 500 grams bread flour 3 1/2 cups
- 40 grams sugar 3 Tablespoons
- 11 grams salt 1 1/2 teaspoons
- 100 grams chocolate chips 1/2 cup
Boil Bath
- 2400 grams water 10 cups
- 24 grams honey 1 Tablespoon
Instructions
Make Dough
- To the bowl of a stand mixer, add all of the bagel ingredients, except the chocolate chips, and mix again on low speed for 5-6 minutes. The dough should be smooth and tacky to the touch.My water was 110 degrees F. The water shouldn't be hotter than 120 degrees F – otherwise this can kill the sourdough starter. You can also mix and knead the dough by hand.150 grams active sourdough starter, 250 grams water, warm, 500 grams bread flour, 40 grams sugar, 11 grams salt
- Remove the dough and knead until smooth. Do so by folding a portion of the dough towards the center and pressing down with the heel of your hand. Repeat about 20 times, then place it in a lightly greased, straight-edged bowl. Cover and leave to rest for 30 minutes.
- After 30 minutes, of resting, pour the chocolate chips on top of the bagel dough. Knead the chocolate chips into the bagel dough by stretching a small piece of the dough up, folding it towards the middle, and pushing the dough down with the heel of your hand. Repeat this for about 30 seconds or until the chocolate chips are incorporated into the dough. Some of the chocolate chips won’t be fully mixed in, and that’s okay. We will correct this during shaping. Cover again and wait until the dough doubles in size.This took about 8-10 hours in my 70 degree F kitchen. The timing depends greatly on the temperature of your dough and environment. The warmer it is, the faster the dough will rise. The opposite is true for cooler kitchens.100 grams chocolate chips
- Once the dough has doubled in size, you can either cover the dough and store it in the fridge overnight, shape the bagels and store in the fridge overnight or proceed to shaping right away.Refer to the Notes before for Make-Ahead options.
- When ready to shape, punch it down to remove all of the air bubbles. Then, place the dough on a clean work surface. Using a bench scraper, divide the dough into 8 equal pieces, about 130 grams each.
- Pull the corners of each piece toward the center, pinch the seams together, flip, and then roll each piece of dough into a tight, round dough ball. Use your thumb to punch a hole in the middle of the dough ball. Some chocolate chips may escape, you can tuck them back in or leave them out. Stretch the dough ball with both thumbs about 2 inches, then place each bagel on a baking sheet lined with parchment paper. Repeat with the remaining pieces of dough.
- Cover the baking sheet with this plastic cover and let the dough rest for its second rise. The final proof is complete when the bagels have grown and look puffy.In my 70 degree F kitchen, this took about 1-2 hours with room temperature dough. If the dough is cold from being in the fridge, the second rise took more like 3-4 hours.
- Once the second rise is almost complete, prepare the boil bath. Fill a large pot with about 10 cups of water. Once the water is boiling, add the honey and stir until it is dissolved. Boil 2-3 bagels at a time, 30 seconds on each side. Use a slotted spoon to remove each bagel and place them on a wire rack. Repeat with the remaining bagels.You will notice that the water will turn brown due to some of chocolate chips melting. This is expected and won't effect the final product.24 grams honey, 2400 grams water
- Once all of the Sourdough Chocolate Chip Bagels have been boiled, place them on a parchment paper lined baking sheet. Preheat the oven to 425 degrees F.
- Bake the bagels for 20-25 minutes or until golden brown with an internal temperature of 205-210 degrees F.
- Cool slightly before slicing. Top with some butter or cream cheese and enjoy!
Notes
Make-Ahead Options:
If you are looking to prepare these Sourdough Chocolate Chip Bagels the night before and bake them the following morning – here are some options and tips! Option 1: Prepare the dough and once it has doubled in size, cover the bowl and chill in the fridge overnight. The following morning, divide and shape the dough into bagels and allow them to rise and get fluffy in a warm place before baking as normal. Since the dough is cool from the fridge, the second rise will take longer to complete, about 3-4 hours in my 70 degree F kitchen. Option 2: Prepare the dough and shape the sourdough bagels the night before. Place them on a parchment-paper lined baking sheet and cover before placing them into the fridge overnight. Pull out the unbaked bagels to allow them to rise and get fluffy in a warm place. In my 70 degree F kitchen, this took about 2-4 hours.Ingredients & Substitutions
- Sourdough Starter – An active and bubbly starter will give you the best rise for these chewy bagels. If you’re looking for something faster, check out my sourdough discard bagel recipe that’s ready to bake in just 2 hours!
- Bread Flour – You technically can use all-purpose flour for these delicious bagels, but I highly suggest making it with bread flour, as it has a higher protein percentage. This allows the dough to rise at great lengths for a more chewy and enjoyable Sourdough Bagel.
- Sugar – I used white sugar for a touch of sweetness, but you can use alternate sugars like cane sugar or honey.
- Chocolate Chips – I used milk chocolate chips, but you can substitute them with any of your favorites like dark, white or even cinnamon chips!
Love the little bits of chocolate in these chewy sourdough bagels. My family loves enjoying them straight out of the oven!
Perfectly delicious!!
So glad you enjoyed this recipe, Devin!
I love your recipes and I love to make them. Thank you for posting them.
Thank you so much for the kind words! I’m so glad you’re enjoying the recipes and taking the time to make them—it truly means more than you know. Thanks for being here and baking along with me!