Chewy Pumpernickel Bagels that are just like your favorite bagel shop! Slightly sweetened with molasses and cocoa powder with a delicious rye flavor that is reminiscent of steakhouse-style pumpernickel bread.
A Quick Look At The Recipe
This is a brief summary of the recipe. Jump to the recipe to get the full details.
Prep Time
30 minutes
Cook Time
20 minutes
Total Time
50 minutes
Servings
12 bagels
Difficulty
Moderate
Calories *
172 kcal per serving
Technique
Make dough, knead, proof, shape, rest, boil, and bake.
Flavor Profile
Perfect bagels made with rye flour, a hint of molasses and cocoa powder.
* Based on nutrition panel
I followed the recipe to a tee, twice. Both batches were perfect⭐⭐⭐⭐⭐
RJ
They are perfectly pumpernickel-y, with a soft, dense crumb and ever-so-slight chew. Toasted or un-toasted, sandwiched or cream cheese-d, they’ve been our source of satiation for breakfast, lunch and dinner the past few days.
Why You Will Love this Recipe
- Perfect pumpernickel flavor like your favorite sandwich shop. The secret to the perfect flavor is in the combination of cocoa powder, molasses, rye flour and a little espresso powder.
- An easy, forgiving bagel recipe. As you can see in my photos below, even if the bagels don’t look pretty before baking, something magical happens in the oven! If you do want to learn how to hand-roll bagels, I show you how in my everything bagels recipe!
- Chewy, perfectly dense bagels with just a hint of sweetness.
- Whole wheat and rye flours add flavor and nutrients.
Ingredients & Substitutions
- Whole Wheat Flour: I use whole wheat flour for the flavor and nutrients, like in my chocolate chip bagels, but you could use bread flour instead. Adding the whole wheat flour with the yeast allows it additional time to hydrate.
- Active Dry Yeast
- Warm Water
- Dark Rye Flour: I love the added flavor and nutrients of dark rye flour, so it is worth seeking out. You can use leftovers in my Russian black bread recipe! You could also substitute medium rye flour.
- Unsweetened Cocoa Powder
- Caraway Seeds: Caraway seeds are a traditional flavor in pumpernickel bread, but you can omit them if you don’t love the flavor. Shhh! I don’t! If you omit them, try topping them with everything bagel seasoning, poppy seeds, or sesame seeds instead!
- Instant Espresso Granules: Some comments have made mention that this recipe came out bitter for them. That is most likely due to the choice of instant espresso or coffee granules. They vary greatly in flavor. It can be reduced or omitted if desired.
- Salt
- Molasses
- Vegetable Oil
- Bread Flour: Just like with Montreal style bagels, I recommend using bread flour instead of all-purpose flour because it contains more gluten for chewy bagels. You can also substitute an equal amount of high-gluten flour, by weight, to compensate for the rye flour like my sourdough discard bagels!
See the recipe card for full information on ingredients and quantities.
How to Make Pumpernickel Bagels from Scratch
Use these instructions to make homemade pumpernickel bagels! Further details and measurements can be found in the recipe card below.
Step 1: In a medium bowl, whisk together whole wheat flour, yeast and warm water until well combined. Let sit for 10 minutes until slightly foamy.
Step 2: Meanwhile, in a large bowl or in the bowl of a stand mixer, whisk rye flour, cocoa powder, caraway seeds, instant espresso and salt until combined. Pour in molasses, oil and yeast mixture. Stir until just combined. Add bread flour and stir just until dough forms.
Step 3: Knead dough by hand on lightly floured surface 10 to 15 minutes, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms; OR, use the dough hook attachment to knead dough in stand mixer for 5 minutes medium low speed, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms (it should pull away from sides of bowl).
Step 4: Shape dough into a ball and transfer to a lightly oiled large bowl. Turn once to coat. Cover bowl with plastic wrap and let dough rise 1 hour to 1 hour 30 minutes until doubled.
Step 5: Meanwhile, heat the oven to 425 degrees F and line two baking sheets with parchment paper or silicone mat, or lightly grease with oil or cooking spray.
Step 6: Punch down the dough to degas. Divide and shape into 12 equal-size pieces (about 3 ounces each in weight). Using your thumb and forefinger, poke a 1-inch hole in the center of the ball and gently stretch to form a hole. Place shaped bagels on the baking sheet and cover with a towel for 10 minutes.
Step 7: Meanwhile, bring a large pot of water to boil. Reduce water to a simmer and place bagels in water one or two at a time. Cook for 30 seconds, then flip over with a slotted spoon and cook for another 30 seconds. Use the slotted spoon to carefully remove the bagels and set on a wire rack. Repeat with remaining bagels. Place bagels on the prepared baking sheets.
If you are adding seasoning, you can either sprinkle the wet bagels with the desired seasoning or dip them in a shallow bowl filled with seeds.
Step 8: Bake bagels for 15 minutes until cooked through and lightly browned on bottom. Transfer to a cooling rack to cool completely.
Recipe FAQs
Homemade bagels tend to keep best for up to 1 day at room temperature, stored in a paper bag. After that, I highly recommend freezing them in a freezer-safe resealable bag, and thawing, slicing and toasting them as needed. You can also slice them before freezing for easy toasting! They will retain freshness for up to 3 months frozen.
Pumpernickel bagels have a light rye flavor from rye flour and a hint of sweetness from molasses and unsweetened cocoa powder. These last two also give it the signature caramel color. Pumpernickel bagels, like rye bread or rieska, can also contain caraway seeds for a slightly anise flavor.
I am a professional baker not a certified nutritionist, but this pumpernickel bagel recipe is a bit healthier than my other bagel recipes due to the addition of rye and whole wheat flour. There is more added sugar from the molasses but I’ll leave the ultimate health test up to you!
Pumpernickel bagels are delicious with cream cheese or butter for breakfast or topped with cream cheese, smoked salmon, onions, and capers! They also make fantastic bagel sandwiches! Use them just as you would pumpernickel sandwich bread or rye bread.
You should make a double batch then slice, butter and toast half to make pumpernickel bagel chips. Then serve those chips with my hot reuben dip!
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If you enjoyed this recipe, please leave a star rating and let me know how it goes in the comments below! I love hearing from you and your comments make my day!
Pumpernickel Bagels
Ingredients
- 1 cup whole wheat flour
- 4 teaspoons active dry yeast
- 1 ¼ cups warm water, about 110 to 115 degrees F
- 1 cup dark rye flour
- ⅓ cup unsweetened cocoa powder
- 1 tablespoon caraway seeds
- 1 tablespoon instant espresso granules
- 1 ½ teaspoons salt
- ½ cup molasses
- 1 tablespoon vegetable oil
- 1 ¼ cups bread flour, plus more as needed
Instructions
- In a medium bowl, whisk together whole wheat flour, yeast and warm water until well combined. Let sit for 10 minutes until slightly foamy.
- Meanwhile, in a large bowl or in the bowl of a stand mixer, whisk rye flour, cocoa powder, caraway seeds, instant espresso and salt until combined. Pour in molasses, oil and yeast mixture. Stir until just combined. Add bread flour and stir just until dough forms.
- Knead dough by hand on lightly floured surface 10 to 15 minutes, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms; OR, use the dough hook attachment to knead dough in stand mixer for 5 minutes medium low speed, adding just enough extra bread flour as needed until smooth, soft, elastic and only slightly sticky dough forms (it should pull away from sides of bowl).
- Shape dough into a ball and transfer to a lightly oiled large bowl. Turn once to coat. Cover bowl with plastic wrap and let dough rise 1 hour to 1 hour 30 minutes until doubled.
- Meanwhile, heat the oven to 425 degrees F and line two baking sheets with parchment paper or silicone mat, or lightly grease with oil or cooking spray.
- Punch down the dough to degas. Divide and shape into 12 equal-size pieces (about 3 ounces each in weight). Using your thumb and forefinger, poke a 1-inch hole in the center of the ball and gently stretch to form a hole. Place shaped bagels on the baking sheet and cover with a towel for 10 minutes.
- Meanwhile, bring a large pot of water to boil. Reduce water to a simmer and place bagels in water one or two at a time. Cook for 30 seconds, then flip over with a slotted spoon and cook for another 30 seconds. Use the slotted spoon to carefully remove the bagels and set on a wire rack. Repeat with remaining bagels. Place bagels on the prepared baking sheets.
- Bake bagels for 15 minutes until cooked through and lightly browned on bottom. Transfer to a cooling rack to cool completely.
Notes
Storage – Store at room temperature for 1 day or in a resealable freezer bag in the freezer for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Like this recipe? Rate & comment below!Before You Go
I hope you enjoyed this delicious homemade bagel recipe. Check out our breakfast and brunch recipes for more inspiration, like these hearty cranberry bagels or go classic with my plain bagel recipe!
Hi Stephanie,
I’m looking forward to trying your recipe this weekend, but after making Everything Bagels from the NY Times recipe, my discovery was the Barley Malt syrup used not only in the initial starter with yeast, but in the boiling water to add that flavor I remember and have been trying to find here in CA…I was wondering if you’ve tried this added ingredient for these sourdough Pumpernickel Bagels? if so, what did you find? If not, I’m wondering if it would add a disharmonious flavor to the Rye Bagel? Thoughts?? Thank you!!
Corinne, I have not yet used Barley Malt syrup for this recipe but I think it could lend a nice flavor!
I made these – they are delicious!
I am so happy to have a pumpernickel bagel recipe with enough pumpernickel flour, but am shocked to see cocoa powder and coffee listed. Is that an original idea or is there more to it that I never knew about?
Julie, In some pumpernickel recipes, the coffee/cocoa powder helps enhance the depth of flavor and dark color we often associate with pumpernickel. You can’t really taste either, but they both contribute to that classic flavor!
Thank you so much for putting this recipe up, I’ve been wanting to try these for ages. I followed your recipe exactly, and the texture came out perfect… so soft and chewy! However, I feel as though it’s a bit too much molasses. I would probably halve the amount if I were to try it again, and I intend to! Hopefully it won’t ruin the texture too much.
Siobhan — So glad you love the recipe (serving them with pulled pork is pure genius). And thanks so much for the tips; I’ll keep those in mind for the next time I bake them myself!
Thank you so much for creating this! I LOVE making rye bagels and am so glad you created a pumpernickel bagel recipe. I made this on Sunday and have been enjoying them with an egg for breakfast and with pulled pork for dinner. I have some brats they’ll go with later this week. This were very easy to make. There are some things I want to share about the recipe with you and your readers. The first is, I think there can be more caraway. The second is that the dough is extremely sticky. Finally, if you have a kitchen aid stand mixer, it may behoove you to purchase a mill attachment if you love rye. I saw this recipe called for rye flour and, out of curiosity, I looked at bob’s rye flour in the store. I decided to keep using my own since Bob’s isn’t nearly as dark as the rye flour we make at home. Plus, you get to keep the bran.
Teffy — I’m not sure if it would turn out with the same flavor/texture, but it’s certainly worth a try!
I’ve never made bagels before because they make me nervous! These look fantastic!
These look absolutely amazing!
I’m having a thing for rye flour at the moment, so this sounds perfect! Do you think I could use coconut oil instead of vegetable?
Gah, envious of these bagels! They look perfectly soft with a little bit of chew. And bravo for making and photographing with the little one running around, not just this post, but always. That would be so hard! Hope to see you soon, xo.