Whole Wheat Everything Bagels

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Savory and delicious these Whole Wheat Everything Bagels are a fun, flavorful and simple breakfast recipe that everyone will enjoy!

Whole Wheat Everything Bagels

Hi everybody! This is Kristie – back again from The Sweet & Simple Kitchen & super excited to be sharing some whole wheat everything bagels with you all!

Fun fact about me; One of my all-time favourite breakfasts is a warm toasted bagel, that has been buttered and smeared with a good dollop of tangy cream cheese. It might sound like the simplest breakfast ever, but there is just something about a good bagel with cream cheese that I can never seem to get enough of. But does a girl ever really need a good reason for why she loves bread or cheese? I think not.

Now while homemade bagels have become something of a regular occurrence around my house, I have to admit that the first time I made bagels I was completely freaked out. The very idea itself was so foreign and daunting to me, that I actually avoided trying it for years.

Whole Wheat Everything Bagels

When I finally got up the courage to try, I had no idea what I was doing, and I thought I was in for a technical battle royal, that would almost definitely end in failure. However, once I actually started making the bagels I realized that not only are they really easy to make, but they are also be so much fun!

There are so many reasons why making these whole wheat everything bagels really is was of my favourite baking projects to date. Everything from seeing the yeast dough rise, to shaping the bagels, to watching them puff up in the boiling water, to the smell that fills your kitchen when you bake them… (this might be my absolute favourite part.)

Bagels really really are such a satisfying baking project, and I would be lying if I said that every time I pull a tray of homemade bagels out of the oven, I’m not beaming with childish pride in my baking accomplishment. Not to mention, there really is nothing quite like eating a fresh, homemade bagel that is still warm from the oven.

Whole Wheat Everything Bagels

So if you have been wanting to try your hand at homemade bagels, I encourage you to give this simple whole wheat everything bagels recipe a try. These bagels have an amazing outer crust, and a chewy interior that is to die for.

I use half whole wheat flour when I make them, because I like a nice hearty bread, but you could definitely sub white flour if you wanted.

This recipe calls for an “everything” topping, but honestly you could customize the topping to whatever suits your fancy. I often top them with just sesame seeds, or a seeded oat mixture, and if I am feeling like something a little sweet, these taste absolutely amazing when topped with cinnamon sugar.

Whole Wheat Everything Bagels

So I definitely encourage you to play around with different flavour combinations to suite your family & just have some a good time baking them, because that really is half the fun!


Whole Wheat Everything Bagels
Whole Wheat Everything Bagels

Whole Wheat Everything Bagels

4.62 from 49 votes
Savory and delicious these Whole Wheat Everything Bagels are a fun, flavorful and simple breakfast recipe that everyone will enjoy!
Servings 8 servings
Prep Time 2 hours
Cook Time 20 minutes
Total Time 2 hours 20 minutes

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  • 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
Course Breakfast
Cuisine American
Calories 390

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About Julie Clark

I'm Julie Clark, CEO and recipe developer of Tastes of Lizzy T. With my B.A. in Education and over 30 years of cooking and baking, I want to teach YOU the best of our family recipes.

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Morgan Butler
3 years ago

hello! is there a better measurement for the amount of yeast to use, rather than ‘a packet’…thanks!

Amy Guillemette
3 years ago

There have been so many positive comments. My dough was very sticky and difficult to work with. At the end the bagels are very flat. I am wondering if you have any thoughts about where I went wrong. I’d love to try this recipe again. Thanks!

3 years ago

5 stars
My friend and I made these yesterday, and they came out wonderfully! It was our first time making bagels, and we are so happy with this recipe. We followed all the steps (our only substitution was maple syrup for molasses), and the bagels are perfectly fluffy inside and crispy outside. Thank you for such a fantastic recipe!

5 years ago

5 stars
I’m a beginner at making bagels – not bread: I’m used to working with yeast, rising times, etc – so I set out on a search for a good whole wheat bagel recipe. This is the third bagel recipe I’ve tried and this is the first that worked out perfectly! I followed the recipe exactly (not typical for me!) and they turned out beautifully. The only change was I took them out after 15 mins and they were perfectly done. My husband said it was the best bagel he has ever eaten. 🙂

3 years ago

It says that cuisine is American, but few of you know that it is actually Jewish.

3 years ago

5 stars
I’ve made quite a few batches of bagels (my new quarantine hobby), but this has been the best recipe I have found to date! Growing up in NY, you get to critique a lot of bagels. To me – it’s all about the “chew.” I just took my first bight of a freshly toasted everything. Holy Friggin’ Delicious!
I think the molasses is what really helped with the overall texture – all that sugar

Thank you so much for sharing this recipe!

3 years ago

Can you substitute sugar for the molasses?

5 years ago

Is there a video or pictures on how to prepare the bagels?

5 years ago

5 stars
Ok, I just made these. The house smells like a NY bagel shop, they look amazing and they taste incredible!! I’m so excited to have this recipe! I do Suzanne Somers weight loss program and I made these legal…I found fat free cream cheese and whipped it with grilled chopped scallions and a little garlic powder…absolutely outstanding!!

Ronnie Brown
8 months ago

4 stars
The recipe calls for instant yeast but my understanding is that instant yeast doesn’t need to be proofed. Does that mean active dry yeast would work just as well in the recipe, as long as you proof it? And if you use instant you don’t have to proof it?

1 year ago

Hi and thank you for the recipe
Can you freeze these ? And if not how many days do they remain fresh ?

2 years ago

3 stars
I’m not sure what went wrong but my bagels came out very flat and lumpy. I’ve made bagels before using a different recipe with great success so I know the problem isn’t technique. The flavor is good.

2 years ago

Anxious to try recipe, but are the nutrition guide lines for large bagels?

2 years ago

Hi there, thanks for the recipe! I’m leaving a comment mainly for anyone that’s looking to try out this recipe- as other commenters said, the dough is super sticky and difficult to work with. The bagels still came out fine, but it would have been nice for the recipe to have addressed this because the whole time I was making them I was convinced I was doing something wrong. Shaping them was nearly impossible! They tasted good but looked a hot mess!

3 years ago

Don’t see how this recipe can work. Most bagel recipes are from 55% to 64% hydration tops.
This recipe is at 77% hydration! The dough would be way too sticky. If use one cup of water plus 2 tbs of water your hydration would come out to 58%. I have not tried the recipe, but from making bagels in the past, that should work better.