The Best Healthy Whole-Wheat Muffins

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 This Recipe Works
Ingredients in These Healthy Muffins
Healthy Muffin Recipes

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

Why This Recipe Works

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.

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

Ingredients in These Healthy 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.

Buttermilk

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.

Cornstarch

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).

Leaverners

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.

Egg

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.

Flavorings

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

Test Kitchen Tips

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.

Healthy Muffin Recipes

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

These Healthy Blueberry Muffins are always a trending recipe here on ZK. They’re made with whole-wheat pastry flour and are loaded with lemony goodness.
One bite of these Healthy Cranberry Orange Muffins and you’ll be transported to a warm and cozy kitchen in the fall. These are scrumptious.
These Healthy Bran Muffins are a sleeper of a recipe! One of our most beloved recipes for many years, it’s a classic for a reason!
If you’re looking for a good gluten-free muffin, check out our Gluten-Free Blueberry Muffins.

FAQs

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?