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    Home » Recipes » Homemade Bagels

    Seeded Whole Wheat Flax Bagels

    Published: May 22, 2021

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    Looking for a bagel that's not only loaded with complex flavour, but also full of fiber? Look no further: Seeded Whole Wheat Flax Bagels!

    A plate stacked with a pile of whole wheat and flax bagels. The top side of each bagel is covered in a mix of seeds - pumpkin, sunflower, flax, sesame, chia, and poppy.

    A few weeks ago, my husband wanted seedy muffins for his weekly breakfast bake.

    It’s something he likes to order when he sees them out in the wild, but then always tells me that if I were to make them at home, they’d be “so much better”.

    In developing a recipe for him for those (I’ll post it in the next few weeks), I happened across a premixed seed product - President's Choice PC Sunflower, Pumpkin & Super Seeds Blend.

    They made fantastic muffin recipe - Seeded Apple Bran Muffins - but also inspired us to make bagels, in somewhat the same vein!

    A plate stacked with a pile of whole wheat and flax bagels. The top side of each bagel is covered in a mix of seeds - pumpkin, sunflower, flax, sesame, chia, and poppy.

    Seeded Whole Wheat Flax Bagels

    Sometimes I’ll just take an ingredient and develop the whole recipe myself.

    Other times, it’s a back and forth thing - I’ll ask him questions and give him options, and take his “wish list” and develop the recipe based on that.

    This time around, we did a “wish list” recipe.

    He chose:

    - Part all-purpose, part whole wheat flour.

    - Add flax meal to the body of the bagel.

    - Seeds both inside and out.

    - Honey as the sweetener (I let him choose between sugar, brown sugar, honey, and maple syrup).

    - Add honey to the boil.

    He wanted it “grainy” and full of fiber, but with a proper bagel texture.

    He loves the crunch and flavour of the seeds, and asked me to go more generous on that, than what he can buy out there.

    From there, I balanced out the flours and the water for the best texture AND flavour, adjusted everything to meet his specs, and went with it.

    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.

    The Seedy Bagel Outcome

    I CANNOT TELL YOU how amazing the house smelled, as these were baking. I made him come down from his work in the attic, just to smell it.

    ... They were a HUGE hit.

    The texture was perfect, he loved the flavour of the seeds with the caramelizing of the honey in the boil/crust.

    He loves “the interest” in it:

    “The wheat, the flax, all the seeds. I don’t know how to describe it. SO good.

    I think the fact that I was eating it on its own, no butter or cream cheese, is telling. Sometimes a bagel is a good base, but it needs something as a compliment.

    This is just amazing all over. It works with cream cheese but doesn’t need it”

    I was shocked to hear that this immediately became his favourite bagel recipe. I had thought for SURE my Smoky Cheese Bagels would be holding that title for a while!

    A close up view of the top of a seeded whole wheat flax bagel. The top is covered in a mix of seeds - pumpkin, sunflower, flax, sesame, chia, and poppy.

    A Note on the Seeds

    While we used a specific pre-mixed seed product for this, you can use your own mix.

    This one contained:

    - Flax seeds
    - Sunflower seeds
    - Pumpkin seeds
    - Chia seeds
    - Shelled hemp seeds

    Which all work well, feel free to use any or all of these, in whatever proportions you like.

    In addition, you can consider:

    - Sesame seeds
    - Poppy seeds
    - Mustard seeds (I like to crush them, and go a bit sparingly with them)

    Finely chopped up nuts would work well in the mix!

    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.

    How to Make Seeded Whole Wheat Flax Bagels

    The full recipe follows at the end of this post, but here’s the pictorial walk-through!

    Start Your Yeast

    The recipe starts out with sugar - in this case, it’s in the form of honey - yeast, and water. This is one of the most important parts of the recipe, so make sure it’s all in place!

    - The water has to be warm, but not hot. You want to encourage the growth of the yeast, without killing it.

    Cool water won’t “wake up” the yeast the way warm does, and it won’t rise as much / quickly.

    Hot water will kill the yeast.

    The sugar feeds the yeast.

    Make sure to use yeast that has been properly stored and is fresh. Very old yeast doesn’t always work.

    Anyway, you mix the three together and leave it for a few minutes, and this is what you should see:

    A two part image showing a 2 cup glass measure full of honey water and yeast, before and after the yeast formed a 1" thick layer of foam on the water.

    Before and after letting the yeast sit for a few minutes.

    When it’s all foamy like this, you’re good to go!

    If your yeast doesn’t foam up in 10 minutes, something went wrong - either the water was too hot /not warm enough, or the yeast was no good.

    No foam means start over again.

    Make Your Bagel Dough

    You can do this by hand, or - like I do - in a stand mixer.

    However you do it, just mix together your flours, flax meal, seeds, and salt.

    A 2 part image showing a metal mixer bowl with the dry ingredients measured into it, then the dry ingredients after being mixed.

    Add the yeast mixture and oil, stirring, until it’s well incorporated.

    A two part image showing the liquid being poured into the mixer bowl of dry ingredients, and after it's been stirred in a little.

    Once it’s all together, you’ll knead the dough. This develops the gluten in the dough, making the dough soft, stretchy, and perfect.

    In a stand mixer:

    Affix a dough hook and just let it go on medium speed for about 7 minutes or so, until it’s smooth and stretchy.

    I start timing once the mixing is done, and all of the extra flour has been “cleaned” off the mixer bowl:

    A three part image showing progression of the dough, from a shaggy mixture, to a smooth dough.

    The progression of kneading the dough.

    By hand:

    Once the dough has come together - and you have all of the flour incorporated into it - dump it out on a clean work surface and knead it.

    Basically, I’ll use the heels of my hands to push down and stretch the dough, fold it over, and repeat for about 15+ minutes.

    It’s a great way to get out some anger, aggression, frustration, or ~feelings~ in general, but it is labourious... so I generally use the stand mixer!

    Anyway, whichever way you go:

    When it’s ready, it’ll be smooth and stretchy.

    You can test readiness by pinching off a small bit of dough, flattening it a bit, and stretching it. If you can stretch it really thin without tearing, it’s done!

    Proof your Dough

    “Proofing” is just letting the dough rise.

    You’ll want a warm - not hot - area to do this.

    As I tend to keep my house nice and cool, I generally cheat at this: I’ll turn the oven on for a few minutes to warm it up a bit, then turn it off and use it as a proofing oven.

    Let it rise - undisturbed - until it’s doubled in volume. Give it a good 45 minutes - 1 hour for this, but don’t leave it much longer than that without checking on it.

    A two part image showing the seeded whole wheat bagel dough in a metal mixing bowl, before and after rising. The dough in the second photo is twice the volume of the dough in the first photo.

    OVERproofing the dough - letting it rise too long / too far - will result in deflated dough, and hockey puck bagels.

    Forming Your Bagels

    Once your initial proofing is done, punch it down and divide it out.

    Punching the dough down removes some of the air, so it’s easier to work with.

    From there, you’ll divide it out to relatively equal portions.

    A two part photo showing the large ball of seeded whole wheat flax dough dumped out on a sheet of parchment, then after it's been divided into 6 balls.

    I usually go with 6 for nice big bagels, but you can do 8 if you’d like them more grocery-store-sized.

    Once they’re divided out, smooth them out into balls.

    I’ll usually smooth it all out towards the edges, and tuck everything under.

    When it comes to making them bagel shaped, there are two main methods:

    1. Roll each lump of dough into a thick “snake” and secure the ends together

    and

    2. Roll each lump into a smooth ball before poking a finger though. Once you have a hole made, stretch the ring of dough out a bit to enlarge the hole.

    A two part image showing a hand holding a ball of dough that's been shaped into a bagel, and then 6 formed bagels on a parchment lined surface.

    Personally, I prefer the latter, so that’s what’s pictured.

    Let them rise for another 10 minutes, as you get things ready to proceed:

    Prepare your Baking Sheet

    Line a baking sheet (2, if you're making more than 6 bagels) with parchment paper, Set prepared pan aside.

    This is also a good time to start preheating your oven.

    Boil Your Bagels

    As your bagels are rising for the second and final time, you’ll get ready to boil them.

    In a large pot, combine water and honey, bring to a boil. I like to lay a sheet of parchment paper out across the other half of the stove, as my work surface.

    Turn heat down a little, allowing water to simmer rather than continue to boil.

    Once the water is boiling, turn the temp down enough to keep it at a gentle simmer. You want to cook the outsides of the bagels gently, not brutalize them.

    2 or 3 at a time, drop your bagels into the simmering water, allow to cook for 1 minute, then flip each and allow to cook for another minute.

    A two part image showing a hand holding a formed bagel over a pot of boiling honey water, and then 3 bagels simmering in the pot.

    Use a big slotted spoon to remove them from the water and allow them to drain well, before placing them on your prepared baking sheet.

    6 boiled seeded whole wheat flax bagels resting on a parchment lined baking sheet.

    Top Your Bagels

    Whisk together your egg and water. This is an egg wash, and it gives a great texture and finish to the bagels - don’t skip it!

    Brush the egg wash over as much of the bagels as are exposed. Tops and sides - you don’t need to flip them to get underneath, though.

    A two part image showing water and an egg in a white coffee mug, then the whisked egg mixture being brushed onto the raw bagels.

    Place seeds in a wide, shallow bowl. One at a time, pick up each bagel, gently invert into the bowl, and swirl around to coat the tops and sides.

    A two part image showing a hand holding a formed bagel over a bowl of seed mixture, then the bagel inverted into that mixture.

    Place topping side up on baking sheets, as you finish each.

    6 seeded whole wheat flax bagels arranged on a parchment lined baking sheet, ready to go in the oven.

    Bake Your Bagels

    Put your pan in the oven and bake until they’re golden brown.

    6 golden brown seeded whole wheat flax bagels arranged on a parchment lined baking sheet, fresh from the oven.

    Enjoy!

    Let them cool a LITTLE when you remove them... but otherwise, you can dig in while they’re still warm.

    Enjoy fresh out of the oven, or let them cool and toast them later!

    A plate stacked with a pile of whole wheat and flax bagels. The top side of each bagel is covered in a mix of seeds - pumpkin, sunflower, flax, sesame, chia, and poppy.

    More Bagel Recipes

    Looking for more fantastic bagels to make? Here are some great options!

    Banana Nut Bagels
    Blueberry Bagels
    Chai Bagels
    Everything Bagels
    Garden Veggie Bagels
    Gluten-Free Bagels
    How to Make Bagels
    Jalapeno Cheddar Beer Bagels
    Marble Rye Bagels
    Mini Bagels
    Montreal Bagels
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    Pumpernickel Everything Bagels
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    Roasted Garlic Asiago Bagels
    Roasted Red Pepper Bagels
    Rye Bagels with Caraway Seeds
    Smoky Cheese Bagels
    Whole Wheat Spinach Bagels

    ... and a few seasonal / holiday options, too:

    Christmas Bagels
    Gingerbread Bagels
    Heart Shaped Bagels
    Hot Cross Bagels
    Maple Pumpkin Spice Bagels
    Paska Bagels

    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.

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    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.

    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.
    Print Recipe Pin Recipe Save Recipe Saved!
    5 from 3 votes

    Seeded Whole Wheat Flax Bagels

    If you're looking for a bagel that's not only loaded with flavour, but also full of fibre, look no further!
    Prep Time30 minutes mins
    Cook Time37 minutes mins
    Rising Time1 hour hr 10 minutes mins
    Total Time2 hours hrs 17 minutes mins
    Course: Bread, Breakfast
    Cuisine: Polish
    Servings: 8 Bagels
    Calories: 447kcal
    Author: Marie Porter

    Equipment

    • Baking Sheet
    • Parchment Paper

    Ingredients

    Dough

    • 1 ⅓ cup Warm Water
    • ⅓ cup Liquid Honey
    • 4 teaspoon Active Dry Yeast
    • 1 ½ cups All Purpose flour
    • 1 ½ cup Whole Wheat Flour
    • ½ cup Flax Meal
    • ½ cup Mixed seeds We used flax, sunflower, poppy, and pepita
    • 2 teaspoon Salt
    • 2 tablespoon Vegetable Oil

    Assembly

    • 3 L Hot Water
    • ¼ cup Honey
    • 1 Large Egg
    • ½ cup Mixed seeds We used flax, sunflower, poppy, and pepita

    Instructions

    • Pour water into a microwave safe bowl. Stir in honey and yeast, allow to stand for 10 minutes – it should get very bubbly.
    • In a large mixing bowl, combine flours, flax meal, seeds and salt. Pour in yeast mixture and oil, stir well to combine.
    • Dump dough out onto a floured surface, knead until soft and elastic, 5-10 minutes. Place dough in a greased bowl, cover with plastic wrap, and allow to rise for one hour, or until doubled in size.
    • Once dough has doubled, punch it down, and divide it out. We divided the mixture into 6 equally sized balls, a large bagel. You can divide into 8 for medium sized bagels, or 10- 12 for smaller bagels.
    • Preheat oven to 350 F. Line 2 baking sheets with parchment paper, scatter cornmeal across if desired. (Optional!)
    • There are two main ways of forming bagels – with roll each lump of dough into a thick “snake” and secure the ends together, or roll each lump into a smooth ball before poking a finger though. Once you have a hole made, stretch the ring of dough out a bit to enlarge the hole. Personally, I prefer the latter.
    • Once you have all of your bagels formed, set them on a baking sheet to rise for another 10 minutes.
    • In a large pot, combine water and honey, bring to a boil. I like to lay a sheet of parchment paper out across the other half of the stove, as my work surface.
    • Turn heat down a little, allowing water to simmer rather than continue to boil. 2 or 3 at a time, drop your bagels into the simmering water, allow to cook for 1 minute, then flip each and allow to cook for another minute. Drain well, place on the parchment lined work surface, allow to cool slightly.
    • Whisk egg together with 1 tablespoon of water, brush over the tops and sides of each bagel.
    • Place seeds in a wide, shallow bowl. One at a time, pick up each bagel, gently invert into the bowl, and swirl around to coat the tops and sides. Place topping side up on baking sheets, as you finish each.
    • Bake for about 37 minutes (for 8), 35 minutes (if you’re making 10-12), or 40-45 mins (If you’re doing 6 large ones), until golden brown.

    Nutrition

    Calories: 447kcal | Carbohydrates: 64g | Protein: 13g | Fat: 18g | Saturated Fat: 4g | Trans Fat: 1g | Cholesterol: 20mg | Sodium: 603mg | Potassium: 398mg | Fiber: 12g | Sugar: 21g | Vitamin A: 32IU | Vitamin C: 1mg | Calcium: 97mg | Iron: 4mg

    A whole wheat and flax bagel, sliced and served on a small plate. The top side of the bagel is covered in a mix of seeds - pumpkin, sunflower, sesame, chia, and poppy.

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    Reader Interactions

    Comments

    1. Rose in Alberta, Canada

      April 19, 2022 at 2:45 pm

      5 stars
      I made the seeded multigrain bagels and absolutely LOVED them. They are a big hit and am already planning to make more this coming weekend. I think I will add some oats to the dough and a sprinkle of flaked salt on the top just before I bake them, to complement the sweetness of the honey.

      Reply
    2. Dee

      January 26, 2023 at 1:09 pm

      These look really good yet I was wondering if there is a way to cut back on the sodium? Just concerned with amount as now my husband has to watch the sodium amount in his foods.

      Reply
      • Marie Porter

        January 27, 2023 at 9:27 am

        You can cut back the salt without affecting the structure, it may just taste a bit flat.

        Reply
    5 from 3 votes (2 ratings without comment)

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