This recipe for 100% whole-wheat muffins has been tested and tested and then tested some more. I’ve honed in on a new technique for baking with whole-wheat flour, which I believe will change the game when it comes to healthy-ish baking. Our “soaker” method creates a 100% whole-wheat muffin that’s uber-tender, light and fluffy, and stays moist for days after baking.

Why These Are The Best Whole Wheat Muffins

Most 100% whole-wheat muffins are riddled with issues—whether it’s being dry and crumbly, rock hard, or even short and stout, most whole-wheat muffins are for the hard-core health nuts. 

Not these muffins—though I do think the health nuts will eat these up too. 

After a variety of tests and many failed methods, I found using a “soaking method” achieved an outrageously tender whole-wheat muffin that was springy, moist, flavorful, and light. Once I honed it on the soaking method, I then needed to refine the ratio of dry-to-liquid both during the soaking stage and mixing of the batter. 

Aside from this revolutionary (in my opinion) method, I also add a bit of cornstarch which is often found in cakes to aid tenderness. Instead of a natural sweetener, I opt for traditional brown sugar but pull way back on the amount. And instead of butter, I use olive oil which keeps the muffins nice and moist, even days after baking.

muffin cut in half and topped with butter on a white plate

Ingredients in Healthy Whole Wheat Muffins

Whole-wheat flour

I was committed to developing a muffin recipe that uses standard whole-wheat flour. I love me some recipes that use whole-wheat pastry flour and white whole-wheat flour, but it’s time we have a muffin that uses good ’ol regular whole-wheat flour.


What used to be the liquid left after churning butter is now a thick and tangy cultured milk product. The slight acidity helps activate the baking soda, and the tanginess adds a nice balance of flavors to the muffin.

If you can’t find or don’t have buttermilk, you can substitute with milk + vinegar. Add 1 tablespoon vinegar to a liquid measuring cup, then pour the milk over top to reach the 1 cup mark. Stir and allow the mixture to rest 10 minutes before using. I will say, the texture of homemade buttermilk is not nearly as impressive as buttermilk from the store, so if you can, use store-bought.

flour, starch, spices, olive oil, vanilla, egg, batter, and sugar measured out and arranged on a table


Cornstarch is a common ingredient in cakes and helps to create a light and tender crumb. If you can’t have corn, you can try arrowroot starch, though we have not tested that (yet). 


You’ll need a bit of baking soda and baking powder for these muffins. We like double acting baking powder.

Brown sugar

Use light-brown sugar and be sure to pack the cup when measuring. We don’t recommend using dark brown sugar as that will alter the amount of liquid in the recipe and likely impact the texture of the 

Olive oil

I love baking with olive oil, and when it’s one of the main flavors I will often use extra-virgin olive oil, like in this lemon tart recipe. However for this recipe, I often prefer regular olive oil for its mild flavor which allows the vanilla, cinnamon and whole-wheat flavor to come through. 


Make sure to use egg labeled as “large.” If you’re using farm-fresh, you can weigh the egg (out of shell) to verify you have the right amount. It should weight 50 grams.

If the egg weighs less than 50 grams (out of shell), crack another egg, whisk the eggs together then weight out 50 grams. Save the rest for a breakfast scramble. 


Ground cinnamon and vanilla add just enough oomph without stealing the show. If you want to play around with flavors, I encourage you to make these once then mix up the spices and extracts. Orange zest, almond extract, ground ginger, and nutmeg are just a few I would try first. 

a muffin, broken in half and arranges on a small white plate with a knife of butter

Tips for Making the Best Whole Wheat Muffins

  • Use a food scale to measure out the ingredients. This is THE most foolproof way for measuring out ingredients. If you don’t have a scale, be sure you fluff the flour before spooning the flour into a measuring cup and leveling with a flat edge. 
  • Coat your muffin tin very well with nonstick spray—this is the only way to ensure the muffins pop out easily. This recipe makes 8 muffins, so before you bake I recommend you wipe out the empty well to avoid the cooking spray from burning. 
  • Use an oven thermometer to understand how hot (or not) your oven is! Most oven run at least 15 degrees hotter or cooler than they display. Adjust the temperature as needed. 
  • Preheat your oven longer. Even if your oven beeps and says it’s preheated, it likely isn’t up to temperature yet. I recommend allowing your oven to preheat for an added 10 minutes before starting to bake. 

More Healthy Muffin Recipes

Check out this list of other healthy muffin recipes that use a variety of wholesome ingredients.


How to tell if a muffin or cupcake is still under-baked?

To test if a muffin or cupcake is done, insert a toothpick or cake tester into the center of a muffin. If it comes out with batter on it, it’s underbaked and needs more time. If it comes out with a few moist crumbs attached, then the muffins are done baking.

Can I use Greek yogurt instead of buttermilk?

We don’t recommend substituting the buttermilk out—it’s an incredibly important ingredient for these muffins.

Any mix-ins you recommend?

We are still testing different mix-ins and will publish those variations as they are tested and passed. A few ideas we are testing include healthy chocolate chip muffins, zucchini muffins, pumpkin muffins, and mini muffins. Any requests?

Whole-Wheat Muffin Recipe

4.85 from 32 votes
Prep Time 5 minutes
Cook Time 15 minutes
Soaking Time 8 hours
Total Time 8 hours 20 minutes
Yield 8 muffins
Category Breakfast
Cuisine American


You get all of the benefits of whole wheat flour (flavor and nutrition) and none of the expected drawbacks (dry, dense or crumbly).


  • 1 ¼ cups (150 grams) + 2 tablespoons (15g) whole-wheat flour, divided
  • 1 cup (252g) buttermilk
  • 2 tablespoons (20g) cornstarch*
  • 1 ¼ teaspoon (5g) baking powder
  • ¼ teaspoon baking soda
  • ¾ teaspoons (2g) ground cinnamon, optional
  • ¼ teaspoon (2g) kosher salt
  • cup (71g) packed light brown sugar
  • ¼ cup (56g) olive oil
  • 1 (50g) large egg
  • 1 tablespoon (15g) vanilla extract
  • Turbinado sugar also called sugar in the raw, for sprinkling on top


  • For the soaker, combine 1 ¼ cups (150g) flour and buttermilk. Stir to combine then cover with plastic or a tight fitting lid and refrigerate overnight (8–10 hours).
    sticky dough mass in a clear glassbowl
  • Heat oven to 425ºF (218ºC). Thoroughly coat muffin tin with nonstick spray.
  • Whisk together remaining 2 tablespoons flour, starch, baking powder, baking soda, cinnamon and salt.
    flour and spices in a small glass bowl
  • In a large bowl, which together brown sugar, oil, egg and vanilla until smooth and pale and most of the sugar has dissolve; 1 minute
    caramel-colored liquid in a glass bowl with a whisk
  • Add soaker to sugar-oil mixture.
  • Whisk soaker into sugar mixture until smooth.
    bubbly caramel-colored batter in a large glass bowl with a whisk
  • Stir in starch mixture to combine.
    caramel-colored batter in a large glass bowl with a whisk
  • Scoop batter by ⅓ cup into muffin tins top with turbinado sugar.
    batter in muffin wells in a muffin tin and topped with sugar
  • Bake 5 minutes then turn oven down to 400ºF (204ºC) and continue baking until golden brown and toothpick inserted in center comes out with few crumbs attached, 8–10 minutes more, rotating muffin tin halfway through baking. (Total bake time 13-15 minutes.)
    8 baked muffins in a 12-tin muffin pan
  • Let muffins cool in muffin tin on wire rack for 10 minutes. Remove muffins from muffin tin and let cool 5 minutes longer. Serve.



Store muffins in an airtight container at room temperature for up to 3 days. After a day or so, the turbinado sugar on the top of the muffins will start to weep—it’s safe to eat, but if you’re making these ahead and plan to serve them a day after baking, skip the sugar topping and instead serve with some honey or honey butter.
If you can’t have corn, you can try arrowroot starch. We have not tested this (yet) but it should work fine.
This recipe makes 8 muffins. We recommend alternating the wells you fill with batter, instead of filling 8 wells side-by-side and leaving 4 empty on the opposite end. Alternating allows heat to more evenly circulate amongst the wells and creates taller, domed muffins. 


Serving: 1muffinCalories: 190kcalCarbohydrates: 27gProtein: 5gFat: 7gSaturated Fat: 1gSodium: 115mgFiber: 3gSugar: 10g
Like this? Leave a comment below!I love hearing from you and I want to hear how it went with this recipe! Leave a comment and rating below, then share on social media @zestfulkitchen and #zestfulkitchen!
muffins piled into a bowl lined with white parchment paper

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About The Author

Lauren Grant is a professional culinary food scientist, food writer, recipe developer, and food photographer. Lauren is a previous magazine editor and test kitchen developer and has had work published in major national publications including Diabetic Living Magazine, Midwest Living Magazine, Cuisine at Home Magazine,,, and more.

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How many stars would you give this recipe?


  1. 5 stars
    I made this recipe using the following swaps: applesauce for oil; flax egg for egg; and thinned Greek yogurt for buttermilk. And yet it was fabulous! We’ve recently had to institute some dietary changes to include whole grains and lower fats and this recipe withstood the swaps and was absolutely delicious. Thank you for the excellent recipe!

    1. Hey Jyll,

      I’m so happy to hear the recipe turned out well with those swaps! Such helpful info for other cooks, thanks for sharing!!

  2. 5 stars
    Delicious muffins. I used some locally sourced hard whole wheat flour and coconut kefir (a grocery mistake that I was trying to use up). Tender, tasty muffins that highlight the flavour of whole wheat and not too sweet.

    1. Hi Nadya! I’m so glad you enjoyed these muffins. They are one of my favorite recipes thanks to the unique and effective soaker method! Glad the coconut kefir worked well in them too.

  3. 5 stars
    I’ve made dozens of whole wheat muffin and bread recipes over the past ~5 years, from all the big name brands (King Arthur, America’s Test Kitchen) to smaller random blogs. This recipe absolutely blew them all out of the water!! I don’t know what magic happens when you soak overnight and use cornstarch (unique as far as I can remember), but these were the first truly tender and moist muffins made entirely from whole wheat that I’ve ever had or made. They had the texture of cupcakes! Incredible!!

    1. Hi Lainey—you just made my entire month! I am so glad you enjoyed these muffins!! They are one of my favorite recipes (and one I’m most proud of). Thanks for trying these and leaving a comment!

  4. I am going to make this recipe this week. For the buttermilk, can I replace vinegar with lemon juice?


    1. Yes, if you plan to make the buttermilk yourself with a milk and an acid, lemon juice should work just fine. I should note—within all of the tests I have done of this recipe, I have always used store-bought buttermilk. I have not tested with homemade buttermilk. If I were to make this with homemade buttermilk, I would use whole milk!

  5. These wheat muffins look gorgeous. Planning to make them this weekend. Would like to know if I can add nuts, dried fruit or fruits to the batter. If yes then how much would you recommend.

    1. Hi Mignonne,
      Great question! I recently tested these with 1 cup frozen blueberries and they didn’t turn out very well. Fresh would probably work better and I might do 3/4 cup next time.
      But in regards to nuts and dried fruit, I would do 1/2 cup chopped nuts OR dried fruit. If you want to do a combo of nuts and dried fruit, I would do scant 1/2 cup chopped nuts and 1/4 cup dried fruit.
      Baking time might be slightly longer, but I would keep an eye on them! Let me know how it goes!

  6. I would love to try this recipe. I have some wholemeal self raising flour that I’d like to use up. Would that be okay for this recipe?

    1. Hi Ann, great question! I worry the leaveners in the self-rising flour will not activate as needed during the baking since they will be soaked with the flour for so long (as written, when using regular whole-wheat flour the leaveners are added post-soak and right before baking. If you do try this with self-rising whole wheat flour, then I would skip adding additional baking powder but still add the baking soda.

      Let me know how it goes!

      1. 5 stars
        I had enough brown sugar to make a double batch. Used the wholemeal self-raising flour and soaked it while I prepared the rest of the ingredients. I still added the extra bicarb and baking soda. I’m GF so couldn’t taste them, but my neighbors and son both said they were very nice. They felt light. I still have some flour left and was thinking of trying some golden syrup as I don’t have any brown sugar left. Any thoughts on that? Thought I might also soak some sultanas in the soak mixture. I’m cleaning out all my cooking ingredients that I’m no longer allowed to eat. Could just throw them out but think it’s nicer to bake them for others.

        1. Hi Ann! Apologies for my delayed reply. Somehow I missed your comment! Happy to hear the self-rising flour worked well! Golden syrup would be delicious in this, I would 1/4 cup and omit the brown sugar all together. If you’ve already tried it with the golden syrup, I’d love to hear how it turned out! What a great way to clean out your pantry AND feed others. Lucky friends and family! 🙂

  7. 5 stars
    These were absolutely amazing!!! I used vinegar and milk to make homemade buttermilk. These have the classic, moist, muffin texture as well as a really great taste. I added chocolate chips to them and did not put sugar on there tops. Looking forward to making whole wheat blueberry muffins next time! Thank you so much for sharing this amazing recipie!

    1. Hi Savannah! Oh my gosh, I so happy to hear you enjoyed these! Also, it’s great to hear homemade buttermilk worked well in these. I’ve been wanting to try these with chocolate chips, so I’m glad it worked well, sounds delicious!