Overnight Sourdough Cream Cheese Stuffed Bagel Bites

Overnight Sourdough Cream Cheese Stuffed Bagel Bites

Growing up in New York, I was spoiled by the abundance of delis selling amazing bagels. It was not until I moved away did I realized, with dismay, the lack of quality bagels (and pizza for that matter!) in other areas.

Although I still can’t get my hands on New York bagels, making bagels at home is the next best thing. I like my bagels loaded with cream cheese– my favorite? Scallion Cream Cheese! And layered with good-quality smoked salmon, sliced tomatoes, and capers. But that is a full-on meal, as a snack, just a schmear of some good old cream cheese suits me just fine.

These bagel bites are perrrfect for snacking but work great as breakfast on the go. Think: road trip. Who has the time for knives and tubs of cream cheese and cutting open a bagel and spreading? That just sounds disastrous to me, not to mention lots of mess and rouge sesame seeds!

This sourdough bagel recipe is naturally leavened and low hassle– just make the dough and let it rise overnight and assemble, boil & bake the next morning. Now that is a #goodmorning.



Get creative and have fun with the bagel bites! I have made a few variations of it by making my own cream cheese mixes. My favorite being: scallion cream cheese, scallion and bacon cream cheese, kimchi cream cheese and jalapeno salsa cream cheese.

Tips for using wetter ingredients (like kimchi or salsa): take care to not add too much moisture. Try “drying” out the ingredients first. For example: to make Kimchi cream cheese, chop but the kimchi real fine then sauté them to remove some of the moisture. Let cool and then generously mix it into a generous amount of cream cheese.

Sourdough Cream Cheese Stuffed Bagel Bites

Bite size stuffed bagel poppers. Naturally leavened and low hassle– just make the dough and let it rise overnight and assemble, boil & bake the next morning. Now that is a #goodmorning.
Prep Time30 minutes
Cook Time25 minutes
Rest Time1 day
Course: Breakfast, Snack
Keyword: bread, sourdough
Servings: 8 bagels



  • 6 g sourdough starter
  • 24 g bread flour
  • 24 g water


  • all levain
  • 128 g water
  • 28 g honey or sugar
  • 5 g salt
  • 250 g bread flour


  • ~100 g cream cheese about half a block or tub

Bagel Toppings (optional)

  • egg wash (1 egg + 2tbsp water) optional*
  • 1/4 cup bagel topping of choice

Water bath

  • 6 cups water
  • 1/8 cup sugar


  • Day 1: Morning, ~10am: Make the levain. Mixing all the ingredients for the levain together. Let rest 8-12 hours.
  • Day 1: Evening, ~10pm: Make the dough. Evenly combine levain, water, honey and salt together. Add bread flour and mix until a rough dough forms. Knead the dough until smooth ~10 minutes by hand. Cover and let rise overnight in a cool place (70-75F) for 8-10 hours.
  • Day 2: Morning, ~8am: Transfer the dough onto a lightly floured surface and divide into 8 even pieces (depending on how big you want your bagel bites to be). Work with one piece at a time, covering the rest to prevent them from drying out.
  • Shape the dough into a rough ball and flatten and shape into a disk. Make the edges thinner than the middle. Using a spoon, take a round scoop of cream cheese and drop it in the middle of the dough. Wrap the edges of the dough together and pinch to seal at the end. Now turn the ball seam side down onto a flour-free area of your work surface and cupping the ball in between palm of your hands and applying gentle pressure, turn the ball clockwise several times to seal the seams at the bottom. You should feel some tension being created between the dough and your work surface. If there isn't, wipe your work surface with a set towel and try again. Check the bottom to make sure it is crease-free, if it is not be patient and continue the clockwise rolling & sealing. Place the dough seam side down on a baking mat. Repeat with the rest. Cover and let rise 1-2 hrs.
    stuffed bagel bites
  • Preheat the oven to 425F. Bring a pot of water and sugar to boil. Gently and gradually lower each dough ball into the water. If you lower them too quickly, they will touch the bottom and stick. If that happens, use a spatula and bring the dough free. Boil the dough for about 45 seconds, flip, and boil for another 30 seconds. You can boil a few at a time but make sure not to overcrowd the pot. Transfer the boiled bagels to a baking mat and repeat with the rest.
  • Make the bagel topping mix. Take the boiled bagels, brush will eggwash (optional), and dip the top into the mix. Alternatively, you can sprinkle on the topping mix. Place it back on the baking sheet and repeat with the rest. Transfer the tray of bagels to the oven and let bake for 25 minutes or until they are golden.


*eggwash gives the bagels a nice sheen.
Recipe for sourdough bagel dough adapted from littlespoonfarm.

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