Sourdough Pumpernickel Bagels

In my humble opinion, pumpernickel bagels are not only the superior bagels, but the *only* bagels.

Which is why it was so disheartening when I learned that they are hard to find outside of the greater New York area.

When I lived in Boston, the few Pumpernickel bagels that I could find did not have that deep earthy taste. They were just bagels dyed brown. The travesty!

What’s a girl to do?

Well, learn how to make them herself!!

I have been experimenting with both yeast and sourdough versions of this recipe, and I find that the sourdough really lends itself to the earthy taste and chewy texture. Plus, this method actually comes together even easier than the yeast version and is extremely forgiving with the rise time. Since sourdough needs a long rest time, it is really difficult to over proof these. I’ve made these in both the summer and winter, left it rise at room temperature for anywhere from 8-12 hours, and even let it rise in the fridge for over 12 hours, and the dough has never failed me! Just make sure that you have a well fed sourdough starter (feed your starter 8-12 hours before starting this recipe), and you are good to go!

And for your efforts, you will get a dense, chewy, earthy, sourdough bagel. YUM.

A mung bean scramble breakfast sandwich!


Makes 6 Bagels
Active Time: 30-45 minutes, Total Time: 1 day


22 grams active sourdough starter
75 grams pumpernickel or dark rye flour
75 grams lukewarm water

380 grams lukewarm water
60 grams molasses, sugar beet syrup, or malt syrup*
15 grams cocoa powder
15 grams wheat gluten
225 bread pumpernickel or dark rye flour
400 grams bread flour
12 grams caraway seeds
8 grams kosher salt

1 tablespoon molasses, sugar beet syrup, or malt syrup


  1. The morning before you want to make the bagels, mix together the active sourdough starter, 75 grams of pumpernickel flour, and 75 grams of water in a large bowl until just combined, and allow to rest, covered for 8-12 hours at room temperature If it is warmer (say above 80 degrees with no air conditioner), aim for eight hours, but if it is colder (below 70 degrees with no heater), aim for 12 hours. If you use a clear bowl, you will be able to see the bubbles forming on the bottom of the bowl. This is a sign that it is fermenting!
  2. After the 8-12 hour period is over, to the same bowl, add the water and molasses and mix everything together until combined.
  3. Add the the rest of the dry ingredients and mix together again.
  4. Once it gets to hard to mix with a utensil, go in with your hands and knead for 10 minutes. Have some bread flour on the side in case the dough is too wet (keep in mind, if you live in a humid environment, you may need to add more flour while kneading than if you were in a dry environment).
  5. You will notice that the dough will become tacky and smooth. Once you get to this stage, it is time for the last rise. Clean the bowl and either grease it or dust with flour (just to make the bowl nonstick).
  6. Allow the dough to rest for another 8-12 hours, covered, at room temperature. If you need to rest it for more than 12 hours, put the dough in the fridge after 8-10 hours to slow down the fermentation.
  7. Once the last fermentation has ended, lightly flour your working surface and remove the dough from the bowl. The dough should be puffy and pliable. Separate into six even pieces and roll out into balls. Don’t worry if you deflate the dough. Pinch the middle of one of the dough balls with your thumb and pointer finger. With your thumb and pointer finger still pinching the middle of the dough, spin the dough until a whole forms in the middle.** Continue for the remainder of the bagels.
  8. Allow the bagels to rest, covered, for 1 hour. Preheat the oven to 425 degrees and boil a large pot (4-5 quarts) of water with 1 tablespoon of molasses.
  9. Once the bagels have finished their resting time (they will look puffy), lower the water so that it is at a simmer. One bagel at a time, use a slotted spoon to dip the bagels in the water. Allow to simmer for one minute at each side. You will notice the bagels start to float when they are ready to be flipped and removed. Continue for all of the bagels.
  10. Place the boiled bagels either on a nonstick pan or a cornmeal dusted bread stone (if using a bread stone, you can preheat it in the oven while the bagels were resting to achieve a crunchy crust). Bake the bagels for 25-30 minutes.
  11. Once the bagels have finished baking, place them on a cooling rack and allow to rest for at least 30 minutes before enjoying.
  12. Toast and spread with vegan cream cheese, peanut butter, avocado, make a breakfast sandwich, or do whatever you want!
  13. These will keep at room temperature in a bread bag for 3-4 days. They take longer to go stale than most breads and can be refreshed in the toaster easily.


*Molasses has a stronger flavor, but I have used it and cannot notice it over the other flavors. Using malt syrup is more traditional, but unless you have more uses for it, you do not need to seek it out! I usually use sugar beet syrup, which can also be used in baking sweets, like muffins.
**Forming the bagels can take some practice. I would recommend looking up videos of professions forming them on YouTube (that’s how I learned!). Alternatively, you can use a silicone bagel mold–not the ones that are for donuts, but the ones that have a handle for dipping the bagels.

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