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How to Make Fluffy Whole Wheat Muffins With Your Favorite Mix-Ins

Whole wheat muffins don’t have a great reputation because there have been so many bad recipes over the years. But bad muffins don’t have to be in your future just because you’ve had them in your past. It is possible to make tender, light muffins with whole wheat flour, and I’ll show you how to do it!

How to Make Delicious Whole Wheat Muffins with Streusel Topping

These muffins are quick to mix up and can be topped with an optional streusel topping, so whole grain doesn’t have to mean less fun. After all, who doesn’t love a bit of streusel? 

Making whole wheat muffins

Whole wheat flour is made by grinding the whole grain of wheat — the bran, germ and endosperm — into a fine flour. White flours, by contrast, are made with only the endosperm. Since it contains the bran and germ, whole wheat flour has less gluten by volume than white flour.

As gluten develops, it creates structure in a dough and helps baked goods to rise well. Since there’s less gluten, whole wheat muffins tend to be dense and heavier than their white flour counterparts.

Whole Wheat Flour

It takes more liquid to help the gluten develop in whole wheat flour, and the rise of these muffins is helped by a little more baking powder than you might use in another recipe. The result is a muffin that rises well and has a tender crumb.

The batter and streusel

The muffin batter mixes up easily using the “muffin method,” where the dry ingredients are mixed together and then the wet ingredients are added all at once. Be sure not to overmix the batter, as overmixing can cause the muffins to become a bit crumbly. 

Using the Muffin Method to Make Whole Wheat Flour

The topping starts by removing a small amount of the dry ingredients after you mix them together. A little bit more sugar is added to the mix, along with a generous dash of cinnamon, before softened butter is cut in to create a mixture that resembles wet sand.

The cinnamon adds a great flavor to the streusel and the extra sugar helps to set it apart from the rest of the muffin. 

How to Make Delicious Whole Wheat Muffins with Streusel Topping

While you do lose a few tablespoons of the dry mix to make the streusel, you will still make 12 muffins. If you choose not to make the streusel and simply make the whole muffin batter, the baking time will not need to be adjusted. The versatility of this recipe is one of the things that I really love about it.

Muffin mix-ins

How to Make Delicious Whole Wheat Muffins with Streusel Topping Mix-In's

These muffins can use up to 1½ cups of almost any mix-ins that you can think of. I recommend using 1 cup of “wet” mix-ins and ½ cup of “dry” mix-ins for a good combination of flavors and textures.

“Wet” mix-ins include any berry or fruit that you might add to a muffin, from diced apples to frozen blueberries. “Dry” mix-ins include chopped nuts, chocolate chips and similar ingredients.

In the muffins shown here, I used whole cranberries and chocolate chunks, a pairing I love. Here are a few more suggestions for flavor combinations you can try:

  • Blueberry Lemon – Add in 1½ cups fresh or frozen blueberries and 1 tablespoon lemon zest
  • Chocolate Chip Pecan – Add 1 cup chocolate chips and ½ cup chopped, toasted pecans
  • Raspberry White Chocolate – Add 1 cup fresh or frozen raspberries and ½ cup white chocolate chips

While there is cinnamon in the streusel, you can also customize these muffins by adding additional spices in with the dry ingredients. 

How to Make Delicious Whole Wheat Muffins with Streusel Topping

Whole wheat muffins

Makes 12


For the muffins

  • 2 cups whole wheat flour
  • 2 teaspoons baking powder
  • ¼ teaspoon salt
  • ½ cup sugar
  • ½ cup brown sugar
  • ¼ cup vegetable oil
  • 1 large egg
  • 2 teaspoons vanilla extract
  • 1 cup milk
  • 1 cup whole cranberries, fresh or frozen (or other berries)
  • ½ cup chocolate chunks (or chocolate chips, toasted nuts)

For streusel

  • 2 tablespoons sugar
  • 1 teaspoons ground cinnamon
  • 1 tablespoons butter, room temperature

Step 1:

Preheat oven to 350 F. Place 12 liners in a muffin tin. In a large bowl, whisk together flour, baking powder, salt and sugars. 

Step 2:

To make streusel: Transfer 3 tablespoons of dry mixture to a small bowl. Add sugar, cinnamon and softened butter, then cut in the butter using a fork until the mixture resembles wet sand. Skip this step if you do not want streusel.

Step 3:

How to Make Delicious Whole Wheat Muffins with Streusel Topping Muffin Tin

In a large measuring cup, stir together vegetable oil, egg, vanilla extract and milk. Pour into dry ingredients and mix until batter has just come together. Add in mix-ins (cranberries and chocolate chips) and fold until well-distributed. Divide batter evenly into prepared muffin pans. Sprinkle streusel over the filled muffins.

Step 4:

Bake for 18-20 minutes, or until a toothpick inserted into the muffins come out clean. Transfer muffins to a wire rack to cool completely. 

Hungry for more? Check out these guilt-free quinoa muffins!

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