There’s nothing quite like a freshly baked chocolate chip muffin. Whether you’re enjoying one as a cozy breakfast treat or a mid-afternoon pick-me-up, these healthy whole wheat chocolate chip muffins are the perfect recipe.

They’re soft, fluffy, and dotted with just the right amount of chocolatey goodness. But here’s the best part: they’re made with wholesome ingredients, including 100% whole wheat flour, and they’re low in sugar.

They’re super simple to whip up—no fancy equipment or complicated steps needed. Let’s get baking!

Why you’ll love this healthy chocolate chip muffins recipe

These muffins are a game-changer for anyone looking for a sweet treat that’s wholesome, delicious, and easy to make.

Whether you’re meal-prepping for busy mornings or whipping up a batch for the family, this recipe is one you’ll come back to again and again. Here’s why:

Healthier ingredients: Made with whole wheat flour and coconut sugar, these muffins strike the perfect balance between indulgence and nutrition. They’re proof that you don’t need to sacrifice flavor for health.
Perfectly sweet: Sweetened just enough to let the chocolate chips shine, these muffins are a treat that satisfies your sweet tooth without going overboard. Each bite is filled with chocolatey goodness!
Easy, and family-approved: This recipe is straightforward and comes together in no time, making it perfect for busy mornings or last-minute baking. But the best thing is that everyone will love them!

Chocolate chip muffins ingredients and some notes

Let’s take a closer look at the ingredients that make these muffins so special.

Each one plays a unique role in creating muffins that are soft, tender, and bursting with chocolatey goodness!

Whole wheat flour: Whole wheat flour adds in extra fiber and nutrients.
Cornstarch: Just a little bit of cornstarch makes these muffins light and tender by softening the whole wheat flour’s texture.
Baking powder and baking soda: This makes the muffins rise beautifully, creating that perfect fluffy texture.
Salt: Balances the sweetness and enhances the overall flavor of the muffins.
Coconut sugar: A natural, minimally processed sweetener that adds a subtle caramel-like flavor and keeps the sugar content lower than traditional recipes.
Eggs: Eggs help bind the batter together and add moisture, resulting in a soft and cohesive muffin.
Yogurt: Adds moisture and a slight tang that complements the sweetness, while also making the muffins extra tender.
Avocado oil: A healthy neutral oil that lets the chocolate chips shine while adding moisture.
Vanilla extract: Adds warm flavor and enhances the natural sweetness.
Chocolate chips: The highlight of every bite! Use your favorite chocolate chips (dark, milk, or semi-sweet) to add rich chocolatey pockets throughout the muffins.

Each of these ingredients works together to create muffins that are delicious, wholesome, and impossible to resist!

How to make whole wheat chocolate chip muffins

Making these healthy chocolate chip muffins is a breeze! With a few simple ingredients and quick steps, you’ll have soft, fluffy muffins ready in no time.

Here’s how to whip them up:

Preheat and Prep. Preheat your oven to 375°F (190°C) and line a muffin tin with paper liners or lightly grease it with cooking spray.
Mix the dry ingredients. In a medium mixing bowl, whisk together the whole wheat flour, cornstarch, leaveners, and salt. This mix creates the perfect base for your muffins.
Wet ingredients. In a large bowl, beat the eggs and coconut sugar together until it is a light caramel color and has increased in volume. Next, beat in the yogurt, oil, and vanilla.
Bring it all together. Mix the dry ingredients into the wet ingredients.
Fold in the chocolate chips. Gently fold in the chocolate chips. Be careful to not overmix.
Bake. Divide the batter evenly among the muffin cups, filling each about ¾ full. Bake for 22 – 25 minutes.
Cool and enjoy. Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely. These muffins are perfect for breakfast, brunch, or as a snack.

Baking tips

Making whole wheat chocolate chip muffins that are tender, fluffy, and perfectly sweet requires just a little know-how.

Follow these tips to ensure your muffins come out bakery-worthy every time!

Beat the eggs and sugar well. Beat the eggs and sugar well before incorporating the other ingredients. This helps the coconut sugar dissolve and helps make the muffins fluffy.
Don’t overmix the batter. When combining the wet and dry ingredients, mix just until the flour is incorporated. Overmixing can lead to dense muffins. A few small lumps in the batter are perfectly fine!
Let the batter rest. Allow the batter to rest for 5 – 10 minutes before scooping it into the muffin tin. This gives the whole wheat flour time to absorb the liquid, resulting in more tender muffins.
Fill the muffin cups generously. For domed muffin tops, fill each muffin cup almost to the brim. Whole wheat batter doesn’t rise quite as much as all-purpose, so a fuller cup ensures tall, beautifully domed muffins.

How to store muffins

Storing your whole wheat chocolate chip muffins properly ensures they stay fresh, moist, and ready for quick grab-and-go breakfasts.

Whether you’ve made a small batch or doubled the recipe, here’s how to keep them at their best for days or even weeks:

On the counter: For short-term storage, keep the muffins in an airtight container or a resealable plastic bag at room temperature. They’ll stay fresh this way for up to 3 days.

In the fridge: If you live in a warm or humid climate, storing muffins in the fridge can help them last longer. Place them in an airtight container to prevent them from drying out, and enjoy them within 5-7 days.

In the freezer: For longer storage, freezing is your best option. Allow the muffins to cool completely, then wrap each muffin individually in plastic wrap or foil. Place the wrapped muffins in a freezer-safe bag or container. They’ll keep for up to 3 months in the freezer. To reheat, simply unwrap and microwave a muffin for 20-30 seconds, or let it thaw at room temperature.

With these simple storage tips, you’ll have delicious, healthy whole wheat chocolate chip muffins ready to fuel your busy mornings!

Conclusion

There you have it—an easy recipe for healthy whole wheat chocolate chip muffins! Whether you’re enjoying them as a quick breakfast or a midday snack these muffins are sure to hit the spot.

I hope this recipe inspires you to whip up a batch and enjoy the satisfaction of homemade goodness. Happy baking!