A bold and flavorful spin on a classic favorite, Pumpernickel Everything Bagels combine the deep, earthy flavor of pumpernickel flour with the iconic crunch of an everything seed topping. With sesame, poppy, caraway seeds, garlic, and onion flakes, these bagels deliver a rich texture and aroma in every bite. Ideal for breakfast, brunch spreads, or hearty sandwiches, this homemade recipe is perfect for bread lovers looking to elevate their baking game.

Why You’ll Love This Recipe

Unique pumpernickel flavor adds a rich, hearty taste to traditional bagels
Topped with a generous everything seed mix for extra texture and crunch
Perfect for slicing, toasting, and layering with your favorite spreads or fillings
Homemade from scratch with no preservatives
Uses both bread flour and pumpernickel flour for the ideal chewy crumb
Boiled and baked for authentic bagel texture
Makes 8 servings—ideal for meal prep or sharing
Easily customizable with your favorite toppings
Freezer-friendly for future breakfasts
Satisfying and nutritious option for any time of day

ingredients

(Tip: You can find the complete list of ingredients and their measurements in the recipe card below.)

1 1/2 cups warm water
1 packet active dry yeast (about 2 1/4 teaspoons)
1 tablespoon sugar
3 cups bread flour
1 cup pumpernickel flour
1 teaspoon salt
1 tablespoon olive oil
1 tablespoon molasses
1 tablespoon sesame seeds
1 tablespoon poppy seeds
1 tablespoon caraway seeds
1 tablespoon dried onion flakes
1 tablespoon garlic powder
1 teaspoon kosher salt (for boiling water)

directions

In a small bowl, dissolve the yeast and sugar in the warm water. Let it stand for about 5 minutes until foamy.
In a large mixing bowl, combine the bread flour, pumpernickel flour, and 1 teaspoon of salt. Create a well in the center and add the yeast mixture, olive oil, and molasses. Stir until a rough dough forms.
Transfer the dough to a lightly floured surface. Knead for 8–10 minutes until the dough becomes smooth and elastic. Add more flour if necessary to reduce stickiness.
Place the dough in an oiled bowl, cover with a damp cloth, and let rise for about 1 hour, or until doubled in size.
Preheat your oven to 375°F (190°C). Bring a large pot of water to a boil and add 1 teaspoon kosher salt.
Punch down the dough and divide it into 8 equal portions. Roll each into a ball, then form into bagel shapes by poking a hole in the center and gently stretching.
Boil the bagels, a few at a time, for 1 minute on each side. Remove and place on a parchment-lined baking sheet.
Mix the sesame seeds, poppy seeds, caraway seeds, onion flakes, and garlic powder. Sprinkle generously over each bagel.
Bake for 20–25 minutes, or until golden brown.
Cool the bagels on a wire rack before slicing and serving.

Servings and timing

Prep Time: 15 minutes
Cooking Time: 30 minutes
Total Time: 1 hour 45 minutes
Servings: 8 bagels
Calories: Approximately 240 kcal per bagel

Variations

Spicy Twist: Add crushed red pepper flakes to the seed topping.
Cheese Topping: Sprinkle shredded parmesan or cheddar over the bagels before baking.
Sweet Version: Omit the everything topping and use cinnamon and raisins in the dough.
Gluten-Free Option: Use a gluten-free flour blend designed for yeast baking.
Mini Bagels: Divide dough into smaller portions to make 12 mini bagels.
Onion-Only Topping: Use only dried onion flakes for a more classic onion bagel.
Whole Grain: Replace bread flour with whole wheat flour for a denser, more fibrous bagel.
Extra Dark: Add a teaspoon of cocoa powder to enhance the color and flavor of the pumpernickel.
Stuffed Bagels: Fill with cream cheese before shaping and baking.
Herb-Infused Dough: Add dried thyme or rosemary to the dough for an herbal note.

storage/reheating

Storage:
Store cooled bagels in an airtight container at room temperature for up to 3 days. For longer storage, refrigerate for up to 1 week.

Freezing:
Wrap bagels individually in plastic wrap and place in a freezer-safe bag or container. Freeze for up to 2 months.

Reheating:
Thaw frozen bagels at room temperature. Reheat by toasting or warming in an oven at 350°F (175°C) for about 10 minutes.

FAQs

Can I use rye flour instead of pumpernickel flour?

Yes, rye flour can be used as a substitute. However, it will result in a slightly different texture and a less intense flavor.

Why do I need to boil the bagels?

Boiling helps set the crust and gives bagels their chewy texture. Skipping this step will result in softer, bread-like rolls.

Can I make the dough the night before?

Yes, you can refrigerate the dough after the first rise and shape the bagels in the morning before boiling and baking.

How do I prevent bagels from sticking to the pan?

Use parchment paper or a silicone baking mat. Avoid greasing the pan, as oil can cause sogginess.

Can I make these without molasses?

Molasses adds depth and color to the dough. You can substitute with dark brown sugar or honey if needed.

How do I get the topping to stick better?

Brush boiled bagels lightly with water before sprinkling the seed mixture to ensure better adhesion.

Can I knead the dough using a stand mixer?

Yes, use the dough hook attachment on medium speed for 6–8 minutes until smooth and elastic.

Are these bagels vegan?

They are vegan-friendly as written. Just confirm your molasses and sugar are free of animal by-products.

Can I toast these bagels?

Absolutely. Toasting enhances the flavor and texture, especially after storing.

What can I serve with pumpernickel bagels?

They pair well with cream cheese, smoked salmon, deli meats, or veggie spreads like hummus and avocado.

Conclusion

Pumpernickel Everything Bagels offer a hearty, homemade alternative to store-bought varieties, combining the deep flavor of pumpernickel with a robust, crunchy topping. Perfectly chewy and endlessly versatile, these bagels are a rewarding baking project for any time of year. Enjoy them warm, toasted, or topped to your taste for a satisfying breakfast or snack.