Healthier Whole Wheat Chocolate Chip Muffins

Jump to Recipe

Looking for a healthier sweet snack or breakfast that won't throw off your healthy eating habits, or give you a sugar rush? These whole wheat chocolate chip muffins are the real deal. Made with 100% whole grain and reduced sugar, but still tastes like a treat.

Partial picture of 4 chocolate chip muffins on a plate with a bite taken out of one.

Homemade muffins are great for breakfast, especially muffins made with wholesome ingredients like whole grains. They are much healthier than traditional muffins made with all purpose flour. Adding chocolate chips gives them a little something special. We like to serve them alongside a bowl of hot cereal like cracked wheat or cream of wheat.

If chocolate chip muffins aren’t doing it for you, then maybe our Healthier Cranberry Orange Muffins, or healthy peach muffins will, they are also made with whole wheat flour.

Jump to:

Recipe Features
Ingredients and Substitutions
Instructions
Serving Suggestions
Variations
Storage
Tips From Our Kitchen
FAQ
Related
📖 Recipe

Buttermilk in muffins is delicious, as Tessa from Handle the Heat agrees in her Ultimate Muffin Guide .

It gives baked goods a moist and tender texture. If you love buttermilk and you’re looking for ways to use it, then you might like our whole wheat buttermilk pancakes, or our chocolate chip pancakes.

Recipe Features

Made with 100% whole grain flour: These chocolate chip muffins are made healthier with whole wheat flour.
One bowl: No-need for two separate bowls here, this chocolate chip muffin recipe only requires one bowl.
Batter can be made the night before: You can mix the muffin batter up the night before and store it in the refrigerator. When you are ready to bake the muffins, fold in the chocolate chips and bake as usual.

Ingredients and Substitutions

Ingredients for whole wheat chocolate chip muffins in original packaging sitting on the counter top.

Whole white wheat flour: We usually use fresh ground hard white wheat flour. High quality store-bought whole white wheat flour works too.
Organic cane sugar: Our favorite is a fine granulated raw cane sugar.
Baking powder: Make sure it is double-acting if you are using the overnight method.
Ground cinnamon: Just enough to give the muffins a subtle cinnamon flavor.
Fine salt: Fine sea salt or any fine textured salt.
Buttermilk: This gives the muffins a tender and moist texture. Keifer will also work.
Butter: You can use salted or unsalted.
Egg: Just a plain chicken egg, make sure it is large.
Pure vanilla extract: Dark or clear Mexican vanilla is our favorite.
Chocolate chips: Because the muffins aren’t overly sweet we like using semi-sweet chocolate chips. You can milk or dark chocolate chips.

See recipe card for quantities.

Instructions

A hand whisking dry ingredients in a clear glass bowl.

In a large or medium bowl whisk the dry ingredients together.

A hand whisking muffin batter in a clear glass bowl.

Add the wet ingredients and whisk until combined.

A hand folding chocolate chips into muffin batter in a clear glass bowl.

Fold in the chocolate chips with a rubber spatula.

Grease a standard size 6 cup muffin tin or line with paper liners.

A hand sprinkling chocolate chips on top of unbaked muffins.

Use a cookie scoop to divide the batter evenly between the muffin cups. Sprinkle the tops with extra chocolate chips if desired.

Whole wheat chocolate chip muffins in a muffin tin on a white towel with black trim.

Set the oven temperature to 400 degrees fahrenheit. Bake for 15-18 minutes or until a toothpick inserted in the center of a muffin comes out clean or with a few crumbs.

Remove the muffins from the pan and serve right away or let cool on a wire rack.

Serving Suggestions

These are the very best served fresh.
You can serve them warm with or without butter.

Side view of muffins in a muffin tin with one broke in half and butter on it.

Variations

To make mini muffins: Use mini chocolate chips and bake for 9-11 minutes. Makes about 24 mini muffins.

Add up to ¼ cup chopped walnuts or pecans.

Storage

Store the cooled muffins in an airtight container for 2-3 day at room temperature.

Tip Place a paper towel in the container with the muffins to soak up excess moisture and keep the muffins from going sticky.

How to Freeze

Wrap individually in a few layers of plastic wrap and place in a resealable plastic bag or freezer safe container. Freeze for up to 3 months. Or, until they are nasty and freezer burned (LOL, kidding!).

Tips From Our Kitchen

Reduce baking time by 1-2 minutes when baking on convection mode.

This muffin batter can be made ahead of time if you use double acting baking powder. Mix up the batter, and refrigerate for several hours or overnight. Fold in the chocolate chips and bake. You may have to bake an additional minute or two to account for the cold batter.

Do not over bake: Overbaking these muffins will result in dry and dense muffins. Even a minute or two over can make them dry.

FAQ

Why are my muffins bitter?

Bitter whole wheat baked goods are usually caused from using flour that is too old. Whole wheat flour contains germ which is an oil, so it will go rancid and bitter after a few weeks on the shelf. Make sure to use fresh, high quality whole wheat flour.

What is the difference between muffins and cupcakes?

Cupcakes are usually sweeter and higher in fat content than muffins. Batter for cakes and cupcakes usually has sugar beaten together with fat to get a light and airy texture then carefully mixed with the other ingredients. Muffins on the other hand usually just mix everything together in one bowl or mix the dry ingredients in one bowl and the wet ingredients in another bowl before mixing the two together.

📖 Recipe

We calculate these nutritional facts using an estimate and they can vary drastically between ingredients used and measuring technique. So, they are not intended for medical use.