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This Homemade Healthy Bagel recipe is made with whole wheat flour. I remember grabbing a bagel with a friend recently, and wondering if I could make healthy homemade whole wheat bagels that would mimic the taste and density of real New York bagels.

There might be “skinnier” bagels out there, like the two ingredient bagel or others made with Greek yogurt or cream cheese, baking powder, or other ingredients. I remember trying one a few years ago and not being impressed with the texture or the taste–it’s just not similar enough to a traditional bagel. These recipes all yielded overly chewy bagels that didn’t quite taste or feel right.

With a lot of trial and error, I’ve managed to create a delicious and healthy bagel that all of my family enjoys. The best part about these whole wheat bagels is that you can make them easily in your own kitchen on your stovetop and oven, in the Ninja Foodi, or in your Instant Pot or other electric pressure cooker.

pinnable image with two pictures of bagels and text

Where’s the Recipe?

Here at My Crazy Good Life we write our recipes so everyone can follow them. We love it when our readers feel comfortable, confident, and successful in the kitchen. The post below includes a step-by-step guide, recipe tips, and healthy eating information.

If you’d like to skip past the ingredient details, recipe tips, nutritional and healthy eating guides, simply scroll down to the bottom where you’ll find the easy to print Whole Wheat Bagel recipe.

Ingredients in these Homemade Healthy Bagels

  • Whole Wheat Flour: I use regular whole wheat flour, not bread flour or white whole wheat flour. Wheat is a great source of fiber. These complex carbohydrates, or slow burning carbs, will keep you full longer.
  • Salt
  • Instant Yeast: instant yeast is key here.
  • Sugar: sugar helps the dough rise.
  • Warm water
  • Cornmeal
  • Egg: an egg and water mixture is used to brush on the boiled bagels before putting any toppings on. If you’re allergic to egg, or prefer not to eat it, you can use plain water.
  • Bagel toppings: I enjoy sesame seeds and poppy seeds.
  • Oil: you’ll need a little oil (olive or avocado will work) to coat the inner liner of your pot).
ingredients needed to make homemade whole wheat bagels

How to make wheat bagels in the Ninja Foodi

I’m loving my Ninja Foodi, and making the bagels in the Ninja Foodi is a breeze. There are two main steps to any bagel after allowing the dough to rise–boiling and baking. You can use your Foodi to boil using the pressure cooker and sauté feature, and then bake them using the air fryer/bake function.

1. Allow dough to rise

  1. Mix yeast with 1 tablespoon of sugar and 1 tablespoon of warm water. Loosely cover with a tea towel and set it to the side for a few minutes. You’ll be looking for some bubbles at the top to know it’s ready–it should take about five minutes.
  2. Mix together salt and flour. After you notice the yeast mixture beginning to bubble, add it to the salt and flour mixture along with the rest of your warm water.
  3. Place your dough on a floured work surface and knead it for a few minutes. You’re looking for it to stop sticking to your hands. If it’s super sticky, add a little more flour. If it seems dry, add a bit of water.
  4. Add the olive oil (or generously spray the olive oil) to the inner liner of your pot.
  5. Place your dough ball inside the pot. Rub the dough on the bottom of the pot so both the top and bottom are coated with a bit of oil. Place a light towel on top of the dough to help it rise.
  6. Turn your Foodi to dehydrate and set the temp to 105 degrees. Set a timer and allow the dough to rise for 30 minutes.

2. Form bagels and allow to rise again

  1. While the dough is rising, get your toppings ready and place some cornmeal on the counter.
  2. After 30 minutes, pull your dough out of the pot and place it on your counter. Quickly fill up your Foodi with water about halfway, set your pressure cooker for 5 minutes and then press start. Allow the water to boil while you’re forming the bagels. This will take about 20 minutes total so you can save significant time by starting this step as soon as the dough is out of the pot.
  3. Divide the dough up into 6, 8, or 10 pieces. (see recipe tips for calorie breakdown)
  4. Shape the bagel dough into circles by rolling out thin strips and securing them at the ends or by making a round ball and poking a hole through the center of the ball of dough.
  5. Place the wheat bagels on the counter and put a thin kitchen towel over them. Allow them to rest for 15 minutes or so.

3. Boil the bagels

  1. After the water comes to pressure, press sauté and allow the water to boil.
  2. Place a few bagels at a time into the boiling water, and allow them to boil for 3 minutes, then flip and allow to cook for 2-3 more minutes. When they’re done, pull them out with big tongs or a large slotted spoon that can cover the entire bagel (using small ones might make your bagels break in half).
  3. Place them on a wire rack while you boil the rest of the bagels.

Pro Tip: If you’re making multiple types of homemade healthy bagels, boil the plain ones first and then the seasoned ones. For example, cinnamon raisin bagel dough will make the water taste of cinnamon. Boil your plain bagels first, then the cinnamon raisin ones.

4. Top the bagels

  1. Mix up your egg and add 2 tablespoons of water. Brush the egg mixture onto your boiled bagels to help the toppings stick. I brush both sides, because I hate sitting down to eat a bagel and being sad that only one side has flavor. Don’t you?
  2. Dip your wheat bagels into the toppings. Be sure to dip both sides for maximum flavor!
  3. To make sure all the toppings are evenly distributed, roll in seasoning, and then use a spoon to sprinkle any seasonings over the top of the bagels that you might have missed.

Tip: If you are allergic to eggs, water will work fine for this step. I’d recommend brushing one at a time with water, then topping.

5. Bake the bagels

  1. Once your bagels are topped, use your air fryer rack inside the Foodi and place 2-3 bagels at a time on the rack. Bake at 350 degrees for 10-12 minutes, flipping halfway through. Keep checking to make sure they don’t burn. Once they are a golden brown color you can take them out of the oven.
  2. Let your bagels cool. If you’re not planning on eating these homemade healthy bagels right away, you’ll want to freeze them for freshness, as they have no preservatives in them. Freeze the leftover bagels individually so they don’t stick together.
collage of images showing how to make skinny bagels

How to make Instant Pot bagels

An Instant Pot or any other electric pressure cooker can be used to warm the dough to help it rise, and then also used to boil the bagels. You’ll need either an air fryer or an oven to bake the bagels after you boil them. You could also use a Mealthy CrispLid with your electric pressure cooker.

You’ll follow the step-by-step guide above, but with a few slight changes.

  1. Allow dough to rise: Set your Instant Pot to the normal yogurt setting, or use the keep warm function.
  2. Form bagels and allow to rise again
  3. Boil the bagels
  4. Top the bagels
  5. Bake the bagels: Bake in the oven or air fryer at 350º for 4-5 minutes, then flip and bake for 4-5 more minutes.

How to make homemade healthy bagels in the stove/oven

Using your stove to boil the bagels and your oven to bake them is a great way to make these skinny bagels. You’ll use most of the techniques used in the directions above, with only a few minor changes when making them in the stove/oven.

  1. Allow dough to rise: Place the dough in a large bowl and cover it with a thin towel. Allow to rise for 30 minutes. If you can get your oven warm for a few minutes and let the bowl of dough rise in there that’s best. Just set the oven to turn on for 2-3 minutes, then turn it off.
  2. Form bagels and allow to rise again 
  3. Boil the bagels: Boil the bagels in a large pot of water on the stove. Boil the shaped bagels using the same technique referenced above.
  4. Top the bagels
  5. Bake the bagels: Preheat your oven to 350 degrees. Place the bagels in the preheated oven on a large baking sheet and bake for 4-5 minutes, then flip and bake for 4-5 more minutes. If you have a convection oven, take advantage of that feature!
6 bagels on a sheet pan

Recipe tips

  • Calorie breakdown: 6 bagels will make each one about 208 calories, 8 bagels will make each one about 156 calories, and 10 bagels will make each one about 125 calories.
  • If your bagels are coming out flat, make sure that you allowed the dough to rise in a warm place for at least 30 minutes (for instant yeast). Go back through your ingredients–are you sure that you added sugar to the yeast instead of salt?
  • If the dough rose, but the bagels ended up flat after the baking process, is could be possible that you didn’t allow the bagels to boil in the hot water long enough.
  • These bagels are not gluten-free.
  • The bagel toppings are endless. There are so many options to choose from. I prefer the classic everything bagels. I buy the seasoning from Costco and the bagels are always delicious.
  • If I’m making only sweet flavored bagels like cinnamon raisin, blueberry, strawberry, etc, I’ll add dry spices (like cinnamon and raisins) to the dough before it rises for the first time. Then I’ll add some honey to the dough along with my wet toppings after they rise the first time.
  • If you’re following a specific diet that requires you to count your sweeteners, like the 21 Day Fix or Weight Watchers, you can easily add your chosen amount of honey and fruit to your bagels depending on how much you want. For example, I add 1 teaspoon of honey to each cinnamon raisin bagel, along with some raisins.
  • Bagels can be stored in the refrigerator for a few days, but the freezer is the best choice for keeping them delicious the longest. These bagels are preservative free so they won’t last as long as the store bought bagels.
  • If freezing: Allow the bagels to cool completely, cut the bagels in half, and place parchment paper or plastic wrap in between cooled bagels when freezing.
image of bowl of homemade bagels

Healthy Eating Plans

Portion Fix

When you divide this recipe to make 10 bagels, each one of these whole wheat bagels counts as one yellow container. If you add honey, raisins, or other sweeteners or fruits to your bagel dough, you’ll want to add that into your counts.

Weight Watchers

When dividing this recipe to make 10 bagels, each bagel counts as 3 points on the 2023 Plan, Blue, Green, and Purple plans. If you add honey, raisins, or other sweeteners or fruits to your dough, make sure to recalculate the points on the Weight Watchers website.

More Healthy Breakfast Recipes

image of bowl of homemade bagels
5 from 9 ratings
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Homemade Healthy Bagels

Created by: Becca Ludlum
Prep Time 15 minutes
Cook Time 20 minutes
Resting time & prep: 45 minutes
Total Time 1 hour 20 minutes
Approximate Serving Size: 1 bagel
Servings 10 bagels
These homemade healthy bagels are delicious and satisfying and have the same properties of a real New York City bagel–they’re dense, chewy, and delicious. If you’ve been wondering how to make wheat bagels, you’re going to love this recipe and making your own budget-friendly bagels at home!

Equipment

  • Ninja Foodi
  • Silpat Mat
  • Metal Pan for Oven

Ingredients 

  • 1 package instant yeast
  • 1 tbsp sugar
  • 1 cup warm water divided
  • 1 tsp salt
  • 2.5 cups whole wheat flour
  • cornmeal for dusting the counter
  • olive oil olive or avocado for coating the inner liner of your pot.
  • 1 egg

Instructions

How to make wheat bagels in the Ninja Foodi:

  • Allow dough to rise:
  • Mix your instant yeast with 1 tablespoon of sugar and 1 tablespoon of warm water. Loosely cover and set it to the side for a few minutes. You'll be looking for some bubbles at the top to know it's ready–it should take about five minutes. 1 package instant yeast, 1 tbsp sugar, 1 cup warm water
  • Mix together salt and flour. After you notice the yeast beginning to bubble, add it to the salt and flour mixture along with the rest of your warm water. 1 tsp salt, 2.5 cups whole wheat flour
  • Place your dough on a floured surface and knead it for a few minutes. You’re looking for it to stop sticking to your hands. If it’s super sticky, add a little more flour.
  • Add the olive oil (or generously spray the olive oil to the inner liner of your pot. olive oil
  • Place your dough inside the pot. Rub the dough on the bottom of the pot so both the top and bottom are coated with a bit of oil. Place a light towel on top of the dough to help it rise.
  • Turn your Foodi to dehydrate and set the temp to 105 degrees. Set a timer and allow the dough to rise for 30 minutes.
  • Form bagels and allow to rise again:
  • While the dough is rising, get your toppings ready and place some cornmeal on the counter. cornmeal
  • After 30 minutes, pull your dough out of the pot and place it on your counter. Quickly fill up your Foodi about halfway, set your pressure cooker for 5 minutes and then press start. Allow the water to boil while you're forming the bagels. This will take about 20 minutes total so you can save significant time by starting this step as soon as the dough is out of the pot.
  • Divide your dough up into 6, 8, or 10 pieces (nutrition calculated based on 10 bagels)
  • Shape the bagels into circles by rolling out thin strips and securing them at the ends or by making a round ball and poking a hole through the middle.
  • Place the wheat bagels on the counter and put a thin towel over them. Allow them to rest for 15 minutes or so.
  • Boil the bagels:
  • After the water comes to pressure, press sauté and allow the water to boil.
  • Place a few bagels at a time into the boiling water, and allow them to boil for 3 minutes, then flip and allow to cook for 2-3 more minutes. When they’re done, pull them out with big tongs that can cover the entire bagel (using small ones might make your bagels break in half).
  • Place them on a drying rack while you boil the rest of the bagels.
  • Pro Tip: If you’re making multiple types of homemade bagels, boil the plain ones first and then the seasoned ones. For example, cinnamon raisin bagel dough will make the water taste of cinnamon. Boil your plain bagels first, then the cinnamon raisin ones.
  • Top the bagels:
  • Mix up your egg and add 2 tablespoons of water. Brush the mixture onto your bagels to help the toppings stick. I brush both sides, because I hate sitting down to eat a bagel and being sad that only one side has flavor. Don't you? 1 egg
  • Dip your wheat bagels into the toppings. Like I said above, change your life and put your toppings on BOTH sides.
  • I brush with egg, then dip into seasoning, roll in seasoning, and then use a spoon to make sure everything is coated.
  • Tip: If you are allergic to eggs, water will work fine for this step. I’d recommend brushing one at a time with water, then topping.
  • Bake the bagels:
  • Once your bagels are topped, use your air fryer rack inside the Foodi and place 2-3 bagels at a time on the rack. Bake at 350 degrees for 10-12 minutes, flipping halfway through. Keep checking to make sure they don’t brown too much.
  • Let your bagels cool. If you don't plan on eating these right away, you’re going to want to freeze them for freshness, as they have no preservatives in them. Freeze the wheat bagels individually so they don’t stick together.

How to make Instant Pot bagels:

  • You can use the Instant Pot or any other electric pressure cooker to warm the dough to help it rise and then boil the bagels. You'll need either an air fryer or an oven to bake the bagels after you boil them. You could also use a Mealthy CrispLid with your electric pressure cooker.
  • Allow dough to rise: Set your Instant Pot to the normal yogurt setting, or use the keep warm function.
  • Form bagels and allow to rise again: No changes need to be made to this step.
  • Boil the bagels: No changes needed.
  • Top the bagels: No changes needed.
  • Bake the bagels: Bake at 350º for 4-5 minutes, then flip and bake for 4-5 more minutes. If you have a convection oven, take advantage of that feature!

How to make wheat bagels using the stove/oven:

  • Using your stove to boil the bagels and your oven to bake them is a great way to make these skinny bagels. You won’t miss a thing if you want to do it this way.
  • Allow dough to rise: Place your dough in a large bowl and cover with a thin towel. Allow to rise for 30 minutes. If you can get your oven warm for a few minutes and let the bowl of dough rise in there that’s best. Just set the oven to turn on for 2-3 minutes, then turn it off.
  • Form bagels and allow to rise again: No changes need to be made to this step.
  • Boil the bagels: Boil the bagels in a large pot on the stove. The rest of the instructions for this step are the same no matter what cooking method you use.
  • Top the bagels: No changes needed.
  • Bake the bagels: Preheat your oven to 350 degrees. Place the bagels on a baking sheet and bake for 4-5 minutes, then flip and bake for 4-5 more minutes. If you have a convection oven, take advantage of that feature!

Video

Notes

Nutrition information is calculated based on this recipe making 10 bagels. 
Healthy eating plans:
21 Day Fix Container Counts:
One of these whole wheat bagels counts as one yellow container. If you add honey, raisins, or other sweeteners or fruits to your bagel dough, you’ll want to add that into your counts.
Weight Watchers points:
When dividing this recipe to make 10 bagels, each bagel counts as 3 points on the 2023 Plan, Blue, Green, and Purple plans. If you add honey, raisins, or other sweeteners or fruits to your dough, make sure to recalculate the points on the Weight Watchers website.

Nutrition

Calories: 113kcal | Carbohydrates: 23g | Protein: 5g | Fat: 1g | Saturated Fat: 1g | Cholesterol: 16mg | Sodium: 239mg | Potassium: 115mg | Fiber: 3g | Sugar: 1g | Vitamin A: 24IU | Calcium: 13mg | Iron: 1mg

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9 Comments

  1. 5 stars
    I made these in the oven and they worked very well! I loved that they use whole wheat flour! Very tasty!

  2. wilhelmina says:

    5 stars
    These bagels are so good! What a great addition to brunch!

  3. Can I use regular white flour or self rising flour instead of whole wheat?
    Thank you
    April

    1. I’ve only tested this recipe with whole wheat flour–white flour will absorb less liquid and definitely give you a different outcome!

  4. Nellie Tracy says:

    5 stars
    These bagels are delicious! I love having bagels for breakfast and can’t wait to make more of them!

  5. Jessica Formicola says:

    5 stars
    This is my family’s favorite bagel recipe! We make them all the time because everyone loves them so much!

  6. Very chewy and easy to make. I used 1 cup white flour and 1.5 cups of 12 grain flour. I find 10 min in the oven is not enough. Seems that the dough is not cooked enough so I left them another 5 min. Also beware of using too much of the Club House Everything Bagel seasoning everywhere. It was too salty. Next time I will just put it on the top or mix it with real seeds (pumpkin, sesame, poppy, flax).

  7. Jennifer Bolton says:

    When did you put the everything seasoning on??
    Or the raisins if making cinnamon raisins?? When do those toppings go in or on?

    1. Sara Anderson says:

      Hi Jennifer,
      In step 19 it gives directions on how to top the bagels :)

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