These Healthy Chocolate Muffins have set a new standard against which all future chocolate muffin recipes will be measured. They are 100% whole wheat, low fat, naturally sweetened, and—despite what you are thinking after reading that suspiciously nutritious sentence—they are so moist, rich, and brownie-like, we’ve been eating them for dessert.

Moist and healthy chocolate muffins with chocolate chips in a muffin tin

These easy chocolate muffins are healthy enough to feel good eating for breakfast before 8 a.m., yet taste indulgent enough to satisfy your sweet tooth at 8 p.m.

I’ve been sneaking bites while I warm up my lunch (does that make them an appetizer too?), followed by more bites with my afternoon coffee (clearly, they are snack worthy as well). Even Ben who (and this is one of the great mysteries of our time) usually passes on muffins with chocolate chips has been snitching these healthy muffins.

These chocolate muffins’ appeal is not limited to adults; they can be readily considered healthy chocolate muffins for toddlers too. My friend brought her to two-and four year old girls over for a visit, and they gobbled theirs up before I’d even poured the milk. When it comes to wholesome recipes, toddler approval is the highest approval of them all.

This recipe came about on a day when I was low on produce and had a hankering for a healthy chocolate breakfast treat. We were out of ripe bananas, so both Chocolate Banana Muffins and Healthy Banana Chocolate Chip Muffins weren’t an option. Chocolate Zucchini Muffins were out for similar reasons (no zucchini on hand).

What I needed was an easy, no fuss, end-of-days healthy chocolate muffin recipe that I could whip up on demand. I think you know where this story leads…

To the consummate, best-ever, healthy chocolate muffin recipe! You can bake these easy muffins anytime a craving strikes.

Let me tell you from experience—once you taste these moist chocolate muffins, the craving strikes all the time.

Moist, healthy chocolate chip muffins in a muffin tin

How to Make the Best Healthy Chocolate Muffins

If you bake healthy muffins regularly, my hunch is you have all of the ingredients you need to bake these chocolate muffins in your pantry right now. Here are the highlights.

The Ingredients

  • White Whole Wheat Flour. My absolute favorite for healthy baking recipes. While whole wheat flour is 100% whole wheat, meaning these muffins are richer in fiber and nutrients than they would be with white, all-purpose flour, and it has a mild flavor, meaning you (and any picky eaters to whom you serve them) won’t notice the swap.
  • Unsweetened Cocoa Powder. For a rich chocolate flavor reminiscent of your favorite brownie.
  • Greek Yogurt. My trick to making these muffins moist, without the need for extra fat. Greek yogurt also adds protein.
  • Chocolate Chips. Because why have a regular chocolate muffin when you can have a DOUBLE chocolate muffin with chocolate chips added?
  • Honey (or Pure Maple Syrup). These muffins are 100% naturally sweetened and made without sugar (the white, more refined kind). Because honey is a liquid sweetener, it adds moisture to the muffins also.
  • Pure Vanilla Extract. A must have in any muffin.
  • Instant Espresso Powder. I add this ingredient almost anytime I’m making a recipe with chocolate. It doesn’t make the muffins taste like coffee; rather, it enhances the intensity of the chocolate flavor (try it sometime; you’ll be amazed!). Instant espresso powder is available at most grocery stores and online here. If you prefer, you can leave it out.
  • Cinnamon. A pinch gives the muffins a subtle warmth.

The Directions

  1. Coat your muffin tin with nonstick spray or line with paper liners.
  2. In a large bowl, whisk together the dry ingredients, and stir in the chocolate chips.
    Dry ingredients in a bowl for making healthy chocolate chip muffins for toddlers or adults
  3. In a medium bowl, whisk together the wet ingredients. Add the wet ingredients to the dry, and stir until the dry ingredients disappear. Don’t over mix!
    Mixing bowl with ingredients for making healthy chocolate chip muffins
  4. Fill each muffin cup almost to the top, then bake at 325 degrees F for 18 to 22 minutes. Let the muffins cool in the pan first, and finish cooling on a wire rack. Then, it’s time to ENJOY the chocolaty goodness!

Recipe Substitutions and Dietary Swaps

  • Gluten Free Healthy Chocolate Muffins. Swap the white whole wheat flour for the same amount of a GF 1:1 baking flour like this one.
  • Vegan Healthy Chocolate Muffins. **Not yet tested, but I think the following would work. If you try it, please report back.** Replace the eggs with flax eggs, use a coconut milk-based yogurt for the Greek yogurt, use maple syrup for the sweetener, and a non-dairy milk for the milk. Be sure your chocolate chips are dairy free also.
  • Healthy Chocolate Muffins with Applesauce. If you prefer, you could try replacing the Greek yogurt with the same amount of unsweetened applesauce or pumpkin puree. (I haven’t tried but imagine this will work; again, please report back if you do!)
  • Healthy Oatmeal Chocolate Muffins. Swap one-fourth of the amount of white whole wheat flour with the same amount of oat flour.

Serving Healthy Chocolate Muffins

While these muffins are delicious straight from the oven, here are a couple ideas for how to serve them:

How to Store and Reheat Healthy Chocolate Muffins

  • To Store. Let the muffins cool completely before placing them in a storage container. Next, line the bottom of an airtight storage container with a paper towel and place the muffins in a single layer on the paper towel. Then, top your muffins with another paper towel to absorb the excess moisture, and store at room temperature for up to 4 days.
  • To Freeze. Individually wrap the muffins in plastic, then place them in a ziptop bag and freeze for up to 2 months. Let thaw at room temperature or rewarm gently in the microwave.
  • For even more storage tips, check out my post on How to Store Muffins and Other Quick Breads.

More Healthy Muffin Recipe Favorites

Recommended Tools to Make Healthy Chocolate Muffins

Moist healthy chocolate muffins for toddlers or adults

These most perfect healthy chocolate muffins set the standard of dessert for breakfast and the standard of breakfast for dessert! If you try the recipe, please let me know how it turns out for you in the comments below. I love to hear from you!

Moist and fudgy healthy chocolate muffins with chocolate chips in a muffin tin
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Healthy Chocolate Muffins

Yield: 12 muffins
Prep Time:
15 mins
Cook Time:
22 mins
Total Time:
40 mins
These Healthy Chocolate Muffins are so moist, rich and fudgy, you'll never believe they are good for you! Made with whole grains, yogurt and no added sugar.

Ingredients

  • 1 cup white whole wheat flour — plus 2 tablespoons
  • 1/3 cup unsweetened cocoa powder
  • 3/4 teaspoon baking soda
  • 3/4 teaspoon instant espresso powder — optional; will result in a more intensely chocolaty muffin
  • 1/4 teaspoon kosher salt
  • 1/8 teaspoon ground cinnamon
  • 1/2 cup semi-sweet chocolate chips — plus optional additional for sprinkling on top
  • 2 large eggs — at room temperature
  • 1/2 cup nonfat plain Greek yogurt — at room temperature
  • 1/2 cup honey — or pure maple syrup
  • 1/3 cup unsweetened almond milk — or milk of choice
  • 1/4 cup canola oil — or melted, cooled coconut oil, light extra virgin olive oil, or melted, cooled unsalted butter
  • 1 teaspoon pure vanilla extract

Instructions

  1. Preheat oven to 325 degrees F. Lightly coat a standard 12 cup muffins tin with nonstick spray or line with paper liners.
  2. In a large mixing bowl, whisk together the dry ingredients: white whole wheat flour, cocoa powder, baking soda, espresso powder, salt, and cinnamon. Stir in the chocolate chips.
  3. In a medium bowl, briskly whisk together the eggs, yogurt, honey, milk, oil, and vanilla. Make a well in the center of the dry ingredients and add the wet ingredients. Gently stir by hand, just until the dry ingredients disappear.
  4. With a muffin scoop or similar, fill the muffin cups 2/3 of the way to the top with batter. If desired, sprinkle on some extra chocolate chips. Bake for 18 to 22 minutes, or until a toothpick inserted in the center of a muffin comes out without any wet batter clinging to it. Place the pan on a wire rack. Let the muffins cool in the pan for 5 minutes, then gently remove them from the pan and place them on the rack to finish cooling completely (don’t leave the muffins in the pan or they will start to steam and become a little soggy). Enjoy!

Recipe Notes

  • TO STORE: Let the muffins cool completely on a wire rack before placing them in a storage container. Next, line the bottom of an airtight storage container with a paper towel and place the muffins in a single layer on the paper towel. Then, top your muffins with another paper towel to absorb the excess moisture, and store at room temperature for up to 4 days.
  • TO FREEZE: Individually wrap the muffins in plastic, then place them in a ziptop bag and freeze for up to 2 months. Let thaw at room temperature or rewarm gently in the microwave.
  • For more storage tips, check out my post on How to Store Muffins and Other Quick Breads.
Course: Breakfast
Cuisine: American
Keyword: chocolate chip muffins, healthy chocolate muffins, healthy muffin recipes, muffins with Greek yogurt, toddler chocolate muffins

Nutrition Information

Amount per serving (1 muffin) — Calories: 193, Fat: 9g, Saturated Fat: 2g, Cholesterol: 28mg, Potassium: 124mg, Carbohydrates: 26g, Fiber: 3g, Sugar: 15g, Protein: 5g, Vitamin A: 40%, Vitamin C: 1%, Calcium: 40%, Iron: 1%

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