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 Must Make

I have wanted to make my own bagels for years and years. I finally bit the bullet and loved every bite!

  • If you’ve always wanted to make bagels at home, give this recipe a try!
  • Making a healthier, whole wheat recipe is a less guilty pleasure.
  • There’s nothing better than the aroma of bread baking in your kitchen….except maybe eating warm homemade bagels.

Ingredient Notes

  • Kitchen Staples – Brown Sugar, Granulated Sugar, Salt
  • Active Dry Yeast – Make sure it hasn’t expired, by looking for the expiration date on the packaging. How to check your yeast if it is close to expiring is listed below.
  • Warm Water – Between 105-115º. Very hot water can kill the yeast.
  • Barley Malt Syrup – Adds sweetness to the bagels. Honey is an easy substitution.
  • Bread Flour – A high-gluten flour that’s ideal for yeast bread recipes.
  • Whole Wheat Flour – A fuller flavored flour containing wheat germ. It has higher fiber, more fat, and more nutrition than regular flour.
  • Cornmeal – for dusting the baking sheet, and coating the bottom of the bagels
  • Baking Soda – Added to the water used to boil the bagels, making it alkaline. Some recipes use baking powder instead.
  • Egg Wash and Toppings – To add poppy seeds, sesame seeds, an everything bagel topping, or grated cheese, first make an egg wash. This is made by whisking an egg with 1 teaspoon of water. Brush this over the proofed bagels, then sprinkle with your topping of choice and bake.
Sliced whole wheat bagel on a round white plate with a red handle knife.

How to Make Bagels

  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 with 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 bagels in water spiked with baking soda before popping them in the oven.

Expert Tips

  • Make sure to check the expiration date on your yeast. It’s no use going through the process of making and shaping the bagels if they don’t rise. It’s best to buy new yeast if it’s close to its expiration date, though most likely, it will still be active.
  • If you have a jar of yeast or an extra packet, you can check it by mixing a packet of yeast (or about 2 1/4 teaspoons) in ½ cup of warm water with ½ teaspoon of sugar. Let rest for 10-20 minutes and if it’s active, the yeast will bubble and expand.
  • Using part bread flour will give the bagels the extra gluten and structure they need.
  • PRO-Tip: If you have a stand mixer, knead the dough with your dough hook. Watch your mixer so it doesn’t overheat.
  • Let the bagels proof until they double in size before boiling.
  • PRO-Tip: Boiling the shaped, unbaked bagels helps set the size as well as thicken the crust. The baking powder addition to the water encourages browning when these bagels are baked in the oven.
  • To add poppy seeds, etc. first brush the bagels with an egg wash so they’ll stick. See ingredient notes above for details.
  • PRO-Tip: Don’t overproof the dough or your bagels will turn out flat or even deflate.
  • You’ll know they’re done when they rise in the oven, are not super heavy (meaning they’ve risen properly), and have a golden brown exterior.
  • PRO-Tip: If you don’t have barley malt syrup, you can substitute honey. Either will add a delicious sweetness to the bagels.

How to Serve

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.They were chewy and fabulous. Bill gave them rave reviews..

  • Toast or just cut in half and smear with cream cheese or butter. Select a flavored cream cheese if you have a favorite.
  • Try them with smoked salmon and a sprinkle of capers.
  • Use them for sandwiches.
  • Top with scrambled eggs and crumbled bacon.
  • Make mini pizzas by topping with pizza sauce, mozzarella and any favorite pizza toppings.

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

Frequently Asked Questions

Are Whole Wheat Bagels Healthier?

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

How Many Calories Are 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 method 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. After testing both, the latter method looked a bit more professional.

How Long Do You Boil the Bagels?

Bagels should be boiled approximately 30-60 seconds per side. Do not overcrowd the pot when boiling them.

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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!


  • 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 ¾ ounces) unbleached bread flour
  • 3 cups (12 ¾ ounces) whole wheat flour
  • 1 tablespoon salt
  • Cornmeal, for dusting baking sheet
  • 1 tablespoon baking soda, 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 2-½ 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 them 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 of baking soda added.  Place a few bagels in the pot at a time and cook for about one minute (30-60 seconds/side).  Remove with a slotted spoon and place on a parchment-lined baking sheet.
  13. Bake for 15-20 minutes or until lightly browned.  Allow the bagels to cool on racks.


Recipe adapted from King Arthur Flour.

Make sure to check the expiration date on your yeast before starting the recipe.

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Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 261Total Fat: 1gSaturated Fat: 0gTrans Fat: 0gUnsaturated Fat: 1gCholesterol: 0mgSodium: 729mgCarbohydrates: 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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