Whole Wheat Everything Bagels
Print Recipe
5 from 5 votes

Whole Wheat Everything Bagels

Savory and delicious these Whole Wheat Everything Bagels are a fun, flavorful and simple breakfast recipe that everyone will enjoy!
Prep Time2 hrs
Cook Time20 mins
Total Time2 hrs 20 mins
Course: Breakfast
Cuisine: American
Servings: 8 servings
Calories: 390kcal



  • 1 package instant yeast
  • 2 tbsp molasses
  • 2 tsp salt
  • 2 cups whole wheat flour
  • 1 1/2 cups all-purpose flour
  • 1 1/2 cups warm water
  • 1 egg to brush on bagels, beaten
  • 1/2 cup cornmeal optional – for the bottom of the bagels
  • 1 pot of boiling water
  • 2 tsp baking soda
  • 1 tbsp granulated sugar

Everything Bagel Topping (Optional)

  • 3 tbsp Sesame Seeds
  • 3 tbsp Poppy Seeds
  • 1 1/2 tbsp Dried Onion Flakes
  • 2 tsp Garlic Seasoning
  • 1 tsp coarse sea salt

Whipped Peppered Cream Cheese

  • 8 ounces cream cheese at room temperature
  • 3/4 tsp coarse pepper



  • In a stand mixer fitted with the dough hook, combine yeast with warm water. Let the yeast proof for 5 minutes until it dissolves and is foamy. Add in flour, molasses & salt and begin mixing with the dough hook. Knead the dough for 5 minutes in the stand mixer or if you are doing it by hand, knead the dough for 10 minutes on a lightly floured surface.
  • Once the dough has been kneaded, place it in a large mixing bowl which has been greased with butter (or oiand allow to rise in a warm place for 1.5 hours or until the dough has doubled in size.
  • Preheat your oven to 425 degrees and line 2 baking sheets with parchment paper.
  • Once the dough has risen, punch it down to release the air and drop it out onto a lightly floured surface. Depending on what size you want your bagels, cut the dough into equal portions…
  • 8 equal portions = 8 large bagels
  • 10 equal portions = 10 medium bagels
  • 12-14 equal portions = 12-14 mini bagels
  • Once you have cut your dough, collect the edges of each individual piece of dough and shape into balls. Once you have shaped all your dough into balls, use your thumb to punch a hole through the center of each ball. Use your fingers to gently stretch the whole to your desired size. Set aside on a baking sheet that has been lined with parchment paper.
  • Once you have finished punching the holes in your bagel dough, allow the dough to rest for 15 minutes in a warm place. The dough will rise up even more during this time.
  • Bring a pot of water to a boil, add in baking soda & sugar. Depending on your bagel size & the size of your pot, place 3-4 bagels into the boiling water at a time. Boil for 90 seconds on one side, flip the bagel and boil for another 90 seconds on the other side. Remove from boiling water with a strainer.
  • Place the bagels onto prepared baking sheet, with cornmeal sprinkled on top of the parchment. Brush the bagels with the egg wash and sprinkle with your desired toppings or just leave them plain. Bake for 20 minutes or until golden brown.
  • Allow to cool for at least 10 minutes before serving. If you want to freeze your bagels, allow them to cool completely and place them in a sealed plastic bag.

“Everything” Bagel Topping

  • In a small bowl, mix together sesame seeds, poppy seeds, garlic flakes & garlic powder – Set aside until ready to use.
  • After you have brushed your bagels with egg wash, sprinkle the topping onto the top of the bagel.

Whipped Cream Cheese

  • In a medium mixing bowl with a stand or hand mixer fitted with the whipping beater, beat the cream cheese on high until smooth and fluffy. Serve just like this or add in pepper and beat until well combined.
  • Serve on a warm bagel with butter & cream cheese.


Calories: 390kcal | Carbohydrates: 55g | Protein: 11g | Fat: 14g | Saturated Fat: 6g | Cholesterol: 51mg | Sodium: 1508mg | Potassium: 340mg | Fiber: 5g | Sugar: 6g | Vitamin A: 410IU | Vitamin C: 0.7mg | Calcium: 138mg | Iron: 3.7mg