These dense and chewy Whole Wheat Bagels rival any bakery version. Making bagels requires a unique process, but you’ll love the results!

Savory and delicious, the addition of whole wheat flour makes for a Healthy Bagel option compared to a standard bagel.

2 whole wheat bagels on a large white plate with one cut bagel topped with a red handle knife with a pat of butter

Why You’ll Love Whole Wheat Bagels from Scratch

I have been wanting to make my own bagels for years and years. Finally, my friend, Annie, of From the Bookshelf, and I decided to do another challenge where we both made the same dish and posted on the same day. Bagels immediately came to mind.

I had a recipe for egg bagels…which have always been a favorite…but I eat almost exclusively whole grain/whole wheat breads these days, so I found this healthier, whole wheat bagels from scratch recipe on the King Arthur Flour site.

Frequently Asked Questions

Are Whole Wheat Bagels Healthier?

Yes, whole wheat bagels are slightly healthier than regular bagels. The whole wheat flour may be enriched with iron, but also has more fiber, and minerals like potassium, selenium, and magnesium.

How Many Calories in a Bagel?

A regular/plain bagel made with white flour has approximately 280 calories. My whole wheat bagels have 260 calories.

How Do You Make the Bagel Hole?

There are two methods. The first, which I used when making these bagels, is to roll a rope of dough, then press the two ends together with the heel of your hand to seal the seam.

Alternatively, make a dough ball, then press a finger through the center and stretch to widen the opening. I find the latter method results in more professionally shaped bagels.

Sliced whole wheat bagel on a round white plate with a red handle knife

How to Make Bagels at Home

  1. Make sure you have bread flour, for extra gluten, and whole wheat flour, for a less processed, healthier component, on hand.
  2. Knead and mix the dough a stand mixer. Using a dough hook and a stand mixer makes quick, easy work of the kneading process.
  3. Shape and proof overnight in the fridge. 
  4. Finally, briefly boil the proofed and shaped dough in water spiked with baking soda before popping them in the ovenn.

PRO-Tip: The boiling helps set the size as well as thickening the crust. The baking powder addition encouraged browning when these whole wheat bagels baked in the oven.

How to Serve Bagels

I sent Bill out for some smoked salmon from Whole Foods so I could test my first bagel with my favorite bagel topping.  As he was checking out, the clerk asked him if he was stopping next door to pick up some bagels to pair up with his seafood purchase. As my biggest supporter, he was happy to brag that his wife whipping up homemade bagels.

These were chewy and fabulous. Bill loved them as did my oldest. They ate theirs with cream cheese and butter, where I love adding smoked salmon and a sprinkling of capers to mine. Shaping was my biggest challenge, but I was pleased with the results of my first attempt.

Check out how to make a Smoked Salmon Platter to go with these whole wheat bagels. And if you’re not a fan of whole wheat breads, check out these Homemade Bagels made with bread flour.

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One Sliced whole wheat bagel on a white plate with a red handle knife topped with a pat of butter

Whole Wheat Bagels

Prep Time 40 minutes
Cook Time 20 minutes
Total Time 1 hour
Yield 14 bagels

Dense, chewy whole wheat bagels made from scratch in your own kitchen! Recipe adapted from King Arthur Flour.


  • 1 tablespoon active dry yeast
  • 2 cups (16 ounces) water, warm, between 105-115º
  • 2 tablespoons light brown sugar
  • 2 tablespoons granulated sugar
  • 1 tablespoon barley malt syrup (I ordered from or honey
  • 3 cups (12 3/4 ounces) unbleached bread flour
  • 3 cups (12 3/4 ounces) whole wheat flour
  • 1 tablespoon salt
  • Cornmeal, for dusting baking sheet
  • 1 tablespoon baking powder, for boiling water


  1. In the bowl of a stand mixer fit with dough hook dissolve yeast in warm water with sugars and barley malt syrup.  
  2. Add one cup of the bread flour and let sit for about 10 minutes. The yeast should start bubbling if it's active (otherwise, you'll need to buy new yeast and start over).
  3. Add the whole wheat flour and mix well.  Add the salt, then the rest of the bread flour one cup at a time, mixing till the dough pulls away from the sides of the bowl.
  4. Continue mixing till the dough is smooth and satiny.  Cover with a damp towel and let rest at room temperature for 20 minutes.
  5. Divide dough into 14 equal pieces.
  6. Take one of the dough pieces and draw up the dough from the bottom, stretch it, and pinch it at the top. Keep pulling the dough up and pinching it until you have a perfectly round, tightly packed ball of dough with a little topknot or pleat at the top.
  7. Turn the dough over so that the knot is against the work surface and push your index finger into the center of the dough.
  8. Wiggle your finger around the hole to stretch it, then start rotating the dough, opening the hole to a diameter of 2 to 2-1/2 inches. The hole should look much larger than what you'd expect from a baked bagel.
  9. Place dough rings on a cornmeal-dusted baking sheet and cover with plastic wrap sprayed with cooking spray.
  10. Place in refrigerator for 12-24 hours.
  11. Remove from refrigerator and let sit at room temperature for 45 minutes. Preheat oven to 450º.
  12. Bring a large pot of water to a rolling boil with 1 tablespoon baking soda added.  Place a few bagels in the pot at a time and cook for about 1-1 1/2 minutes.  Remove with slotted spoon and place on parchment-lined baking sheet.
  13. Bake for 15-20 minutes or until lightly browned.  Allow the bagels to cool on racks.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 261Total Fat: 1gSaturated Fat: 0gTrans Fat: 0gUnsaturated Fat: 1gCholesterol: 0mgSodium: 564mgCarbohydrates: 55gFiber: 2gSugar: 6gProtein: 7g occasionally offers nutritional information for recipes contained on this site. This information is provided as a courtesy and is an estimate only. This information comes from online calculators. Although attempts to provide accurate nutritional information, these figures are only estimates. Varying factors such as product types or brands purchased can change the nutritional information in any given recipe. Also, many recipes on recommend toppings, which may or may not be listed as optional and nutritional information for these added toppings is not listed. Other factors may change the nutritional information such as when the salt amount is listed “to taste,” it is not calculated into the recipe as the amount will vary. Also, different online calculators can provide different results. To obtain the most accurate representation of the nutritional information in any given recipe, you should calculate the nutritional information with the actual ingredients used in your recipe. You are solely responsible for ensuring that any nutritional information obtained is accurate.


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