Pumpernickel Bagels

Pumpernickel Bagel Crumb - Peter Reinhart

This is pumpernickel in the American tradition where a little help from wheat flour (for structure) and molasses (for color) are added to coarsely ground rye flour. The dark color characteristic of German pumpernickel breads is achieved through the Maillard reaction where loaves are cooked low and slow for 16 to 24 hours. This baking method deeply caramelizes the pumpernickel flour and develops an intense flavor (more on that in a later post). I would call German pumpernickel the barbecue of breads but depending on who’s around, I suppose you could call barbecue the pumpernickel of meats.

A lightly toasted pumpernickel bagel is a fine alternative to my other breakfast bread. Avoiding the vending machine until lunchtime is a cinch with this 100% whole grain bagel and its pronounced flavor really wakes up your taste buds in the morning.

The flavor and texture is completely different depending on how soon the bagels are eaten after baking. Within fifteen minutes the crust is pleasantly crisp but hours later a more bagel-like chewiness comes through.

makes 6 bagels
recipe adapted from Peter Reinhart’s Whole Grain Breads, winner of the 2008 James Beard Award for Best Baking/Dessert Book. Buying cookbooks as soon as they get released isn’t such a bad idea after all.

Whole Grain Pumpernickel Bagels

For the soaker:

3/4 cup plus 2 tablespoons (4 ounces) whole pumpernickel/coarse rye flour
3/4 cup plus 2 tablespoons (4 ounces) whole wheat flour
1/2 teaspoon salt
1/2 cup plus 2 tablespoons (5 ounces) water
3 1/2 teaspoons barley malt syrup
2 1/4 teaspoons molasses


  • I don’t recommend it, but you can use honey instead of the barley malt syrup. Bagels just don’t seem right without it.
  • I used blackstrap molasses, which some may find a bit heavy. Lighter types of molasses will do just fine, of course. The alternative to molasses is sorghum syrup, which is something I’ve never used before.

Mix the soaker ingredients until evenly hydrated. Cover and leave at room temperature for 12 to 24 hours.

For the biga:

1 3/4 cups (8 ounces) whole wheat flour
1/4 teaspoon instant yeast
1/2 cup plus 2 tablespoons (5 ounces) water, at room temperature

Mix the biga ingredients until a rough ball of dough is formed. Knead the dough for about 2 to 3 minutes to ensure that the dough is evenly hydrated. Cover and refrigerate at least 8 hours and up to 3 days.

Pumpernickel Bagel Biga and Soaker - Peter Reinhart
which one has molasses in it?

For the final dough:

all of the soaker
all of the biga
2 1/4 teaspoons instant yeast
2 tablespoons (1 ounce) water, at room temperature
5/8 teaspoon salt
7 tablespoons (2 ounces) whole wheat flour


  • I like my bagels, especially pumpernickel, matte and unassuming, so I usually skip the egg wash and toppings. Feel free to use anything from salt to diced onions.

Cut up the soaker and biga into small pieces and combine with all of the final dough ingredients. This is Reinhart’s epoxy method for whole grain dough, also used in the anadama formula.

Knead the dough for 3 to 4 minutes. Dough with rye flour tends to be sticky but this dough should be fairly stiff. Adjust with additional whole wheat flour if necessary. Let the dough rest for 5 minutes then knead again briefly for about 1 minute.

Place the dough in a lightly oiled bowl and cover. Let rise at room temperature for 45 to 60 minutes or until 1 1/2 times its size.

Divide into 6 equal portions.

Divided Pumpernickel Bagel Dough

Let the pieces of dough rest for 5 minutes before shaping into ropes.

Pumpernickel Bagel Dough ropes

Wrap the ropes around your knuckles such that the ends are overlapping over your palm. Roll the ends on an unfloured counter to seal.

Shaped Pumpernickel Bagels

Preheat the oven to 500°F. The bagels will be ready to boil within 20 to 30 minutes of shaping. You didn’t think we’d skip that step did you?

To boil the bagels:

2/3 cups baking soda
10 cups water


  • Reinhart’s boiling water calls for “4 inches of water” and 2 teaspoons of baking soda. This just doesn’t seem like enough alkalinity to replace the much stronger and potentially dangerous lye bath. I went with the stronger alkaline solution in Alton Brown’s pretzel recipe where more precise measurements are also suggested.

Bring the water to a boil in a wide pot. Add the baking soda slowly to keep the foam from overflowing. Lower the heat to maintain a gentle simmer. Think of it as poaching instead of boiling.

Boil the bagels for a total of 1 minute, turning halfway through.  The bagels should float within 30 seconds.  Transfer the boiled bagels to a sheet pan.

Boiled Pumpernickel Bagels, ready for baking

Bake the bagels. Place the sheet pan in the oven and immediately lower the temperature to 450°F. Bake for 15 minutes, rotate the pan, then bake for another 10 to 15 minutes, until the bagels are dark brown.

Transfer the bagels to a cooling rack and cool for at least 15 minutes.

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22 Responses to “Pumpernickel Bagels”

  1. MyKitchenInHalfCups says:

    Those could win anybody’s heart!
    Wonderful color and crumb!

  2. rainbowbrown says:

    These look great. I haven’t tried this recipe, but I think now that I should. Good call with the boiling water solution change.

  3. Ralph says:

    Those bagel look great and sound very healthy. I will try them. Great post with informative pictures.
    In Germany ‘ Laugen Brezeln ‘, German soft pretzels are first cooked in a sodium hydroxide solution. Maybe I will try that with the bagels. Thanks for this post!

  4. Sherrie says:

    WOW, great job, looks divine!

    This great product is a MUST HAVE in your kitchen if you love to bake, highly heat resistant and extremely durable!!!


  5. Thanks guys!
    I’ve always wanted to use Lye/Sodium Hyroxide for pretzels or bagels but always chicken out at the last moment. They’re usually available at the local oriental groceries.

  6. Natashya says:

    I cannot believe you made those at home. They are perfect! Great job.

  7. Sarah says:

    I’ve always wanted to make bagels, delicious looking ones here! Thanks for the recipe!

  8. Eggy says:

    these are a staple of my kitchen. i think by far this is my most favourite recipe from your blog. as i type this i have the biga and soaker ready in my kitchen to make a batch of mini-bagels for next week’s classes!

  9. Sarah says:

    These are beautiful, but one obvious question. How do you store them?

  10. Eggy, it’s easily my bagel recipe of choice, too. Safe to say the deli around the block won’t have anything like this :)

    Sarah, I usually store these bagels in ziploc bags at room temp or in the freezer. If freezing, I pre-slice so they’re easier to toast up later.

  11. Robert Giustra says:

    The author calls for “Whole” pumpernickle & wheat. Does that mean “uncracked” the whole kernel?

  12. Robert, the pumpernickel and wheat flours are indeed made from the whole grain, but ground into a fine flour (pumpernickel will be a lot more coarsely ground than the wheat). I hope this clarifies things!

  13. alkaline water says:

    My mom recommended converting too alkaline water instead of regular water. Something aboutalkalizing or something along thos lines is supposed to much healthier for you.

  14. bestbuy says:

    these are a staple of my kitchen. i think by far this is my most favourite recipe from your blog. as i type this i have the biga and soaker ready in my kitchen to make a batch of mini-bagels for next week’s classes!

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  16. freeboard says:

    Thank you for this article. Waiting for next one.

  17. Cara says:

    Hello and thank you for this recipe. I cook a lot of bagels and desperately needed a pumpernickel recipe. I am noticing that the baking temp seems really high to be cooking these little breads for 20 to 25 minutes. My bagels are normally done within 12-15 minutes at a lower temperature. Can you confirm that the values stated here are correct please?
    Thank You.

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  22. Chris says:

    Great recipe, but 2/3 c of sodium bicarbonate is waaa-aaay to much. The first time I made a batch the bagels came out with a HEAVY chemical twang. I’ve cut it down to a loose 1/4 c and thoroughly enjoy the results.

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