Pumpernickel Bagels

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.

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

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!

4.25 from 4 votes

Pumpernickel Bagels

By Stephanie Wise

Chewy pumpernickel bagels that are just like your favorite bagel shop in 2 hours! Slightly sweetened with molasses and cocoa powder with a delicious rye flavor.

Servings: 12 bagels

Prep Time: 30 minutes mins

Cook Time: 20 minutes mins

Total Time: 50 minutes mins

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Ingredients 

1x2x3x

• ▢ 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

US Customary – Metric

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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

Yield – 12 bagels
Storage – Store at room temperature for 1 day or in a resealable freezer bag in the freezer for up to 3 months.

Nutrition

Calories: 172kcal, Carbohydrates: 36g, Protein: 5g, Fat: 2g, Saturated Fat: 0.5g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 0.01g, Sodium: 298mg, Potassium: 339mg, Fiber: 4g, Sugar: 11g, Vitamin A: 3IU, Vitamin C: 0.1mg, Calcium: 43mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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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!