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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. (same with Chocolate Oatmeal!), 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). Plus, I wasn’t quite in the mood for my rich and decadent Chocolate Muffins.

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!

Healthy Chocolate Muffins

4.81 from 206 votes
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.

Prep: 15 minutes
Cook: 22 minutes
Total: 40 minutes

Servings: 12 muffins


  • 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


  • Preheat oven to 325 degrees F. Lightly coat a standard 12 cup muffins tin with nonstick spray or line with paper liners.
  • 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.
  • 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.
  • 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!


  • 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.


Serving: 1muffinCalories: 193kcalCarbohydrates: 26gProtein: 5gFat: 9gSaturated Fat: 2gCholesterol: 28mgPotassium: 124mgFiber: 3gSugar: 15gVitamin A: 40IUVitamin C: 1mgCalcium: 40mgIron: 1mg

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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  1. I LOOOOOOOVE! They came out so tasty and fluffy! It’s as sweet as it should be. I’m obsessed with this recipe! I used low fat cow milk, olive oil, full fat Greek yogurt, honey and I didn’t vanilla extract and espresso powder cause I didn’t have them but they came out so perfectly! It’s also so easy to make despite having many ingredients I only used 2 bowls, 2 spoons and one cup! Sooo easy! I ate 5 of them in a couple hours! Thank you for the recipe and congrats!5 stars

  2. Terrible. Muffins didn’t rise. I have a feeling I fell into the trap of making their recipe twice as it’s what comes up first with good reviews on google YET the same thing happened!! But only good reviews are posted? I’m so disappointed and what a waste of ingredients!1 star

    1. I’m sorry to hear you had trouble with the recipe, Becky. There are a few reason why muffins won’t rise. Over-mixing the batter, old, expired, or insufficient baking soda, the oven not heating properly or not filling the muffin tins properly. It’s really hard for me to know exactly what went wrong without being in the kitchen with you. Also we allow all kind of comments to be posted on our site. For this particular recipe you don’t find a lot of negative reviews because there haven’t been any that said their muffins didn’t rise. Hope this helps!

  3. A great not-too-sweet muffin, great for guiltless breakfast or snack! Didn’t have espresso powder but think that would have made them even better! Added some quick oats I needed to use up and turned out great.5 stars

  4. Just made these today and they turned out scrumptious! Very moist and flavourful with just the right amount of sweetness. My husband had one bite and said, “Wow, this is so decadent!” My preschooler requested more after I gave him a piece. These are a hit. Thank you for the wonderful recipe. Love the addition of Greek yogurt for some extra protein!5 stars

  5. Success! I made mine with gluten free flour, cacao powder, and coconut oil instead of canola. It’s a great muffin! Nice texture and rich flavor.4 stars

  6. So moist and chocolatey! They didn’t taste like “healthy” muffins. I purposely over filled them to make eight huge bakery looking muffins. Baked for 18 minutes and they rose beautifully. Thanks for the recipe will definitely be my go to from now on :)5 stars

  7. Can’t fault this recipe. A friend made these and brought one for me to try. I ended up making two batches in a day. They are that good. My kids love them. I’ve tried quite a few muffin recipes and a lot of the time they turn out quite dry. This recipe was not like the others. A keeper!!!5 stars

  8. I used whole wheat flour, applesauce instead of yogurt, and extra virgin olive oil and maple syrup instead of honey. I tripled the recipe. I must have made them too big because I got 30 muffins instead of 36. But thats ok. They are nice size for breakfast. 2nd time making them. They are so yummy!!! Nice and fluffy!! Everyone in my family likes them.5 stars

  9. These are the best chocolate healthy muffins, they rise up so well and they’re so easy to make. Definitely recommend 😁5 stars

  10. These are super. I make these substitutions: swap the honey/maple syrup for 1/2 cup of stevia maple flavored syrup. Also add a 1/2 teaspoon of stevia granulated. Lowers the glycemic index hit a bit, I think?5 stars

  11. I have been trying out different muffin recipes that are healthy, to keep in the freezer on mornings that I don’t really feel like making anything, or if I just randomly crave a muffin.

    These turned out amazing! I used cacao powder instead of cocoa. I loved the slight hint of cinnamon in these too! Will be making this regularly :) I bet some dried cherries or nuts would be nice to add in as well.5 stars

  12. Hi Erin, thank you so much for this recipe!! To be honest I almost made it every week since spring this year 😆 sometimes I used all purposed flour when I ran out of whole wheat flour and I didn‘t use espresso since it was made for my almost 3 years old and for her friend too. She‘s so obsessed with this muffins! I also use 1/2 tsp baking soda + 1 tsp baking powder (it’s just I always have this amount of mix for any muffins that I made) and it was always turned out perfectly fluffy and moist. Once again thank you so much! It‘s really a hit in our home!! ❤️5 stars

    1. I’m so confused Sophie, because I see it on my end. The recipe is in the recipe card, right above the area where you commented. You can also click the “jump to recipe” button at the top of the screen to help get you there faster. Could you please check again!

  13. Followed the recipe pretty closely. Used regular salt and 1% milk. And low fat Greek yogurt. I liked the espresso addition. Definitely adds a twist. I think next time I might add just a little more honey than what’s called for. I like them a little sweeter. These are tasty.5 stars

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