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.
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5 Star Review
“Great recipe! I’ve tried other healthy recipes and the texture has been off. This one has great flavor and is very moist. Will definitely keep this one!”
— Lisa —
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.
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.
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.
Key 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
Coat your muffin tin with nonstick spray or line with paper liners.
In a large bowl, whisk together the dry ingredients, and stir in the chocolate chips.
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!
Fill each muffin cup almost to the top, then bake at 325°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!
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:
Toppings. A dollop of nut butter or Greek yogurt is scrumptious and extra filling.
Fruit. A side of fresh fruit with these muffins makes a sunny, well-rounded breakfast.
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.
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.
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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!
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.
Hi, I’m Erin Clarke, cookbook author and the home cook behind Well Plated. I’ve helped millions of people cook healthier meals that actually taste amazing and sold over 190,000 books! I’m here to help you save time, dirty fewer dishes, and feel great about what you’re eating, without overthinking it. Welcome!
We LOVE this recipe! It’s become a regular for us. I use whole spelt flour, non-dairy yogurt, olive oil and maple syrup as substitutes. Turns out great!
A fun tip if you have kids: Bake the entire recipe in a round cake pan (8 or 9 inch), but leave out the chocolate chips during baking. When it’s done, remove from the oven and top with the chocolate chips and smooth them around the top of the cake when melted, like frosting. It then seems like gooey, chocolate cake is for breakfast! 😉
Delicious! I added 4 tbsp chia seeds + more milk and coco powder. Also swapped choco chips with chopped nuts and a tiny bit of oats. Going to be making these weekly! Thank you for this wonderful recipe.
This recipe was so good and I will defiantly be making this again. (I forgot to add extra chocolate chips) and so I wish there was a little more included in the recipe.
Great recipe! I’ve tried other healthy recipes and the texture has been off. This one has great flavor and is very moist. Will definitely keep this one!
I realized I didn’t have enough eggs so I used half a cup of unsweetened apple sauce instead. Worked like a charm! So that’s another way to veganize them too!
(Notes for anyone else trying—I didn’t use espesso powder and did use extra virgin olive oil instead of canola oil, don’t know if using espresso powder and canola oil would interfere with the apple sauce in any way)
Thanks for a delicious *and adaptable* recipe, Erin!
Hi Stephanie, yes! Anytime you see it written “white whole wheat flour” you can substitute with all-purpose flour or an 1:1 gluten free flour. Hope this helps!
I have made these twice now. The flavor is amazing, but they sink in the middle when I take them out of the oven.i used almond flour, would that make a difference?
Hi Judith, we’ve not tested these with almond flour but that is likely the cause. When using oat flour this is what we recommend and since it is interchangeable with almond flour I’d start here: “Swap one-fourth of the amount of white whole wheat flour with the same amount of oat flour.” Let us know how it goes!
I made these into mini muffins & swapped the chocolate chips for a chopped up dairy milk bar (1/2 of the chocolate called for) and they are SO delicious. Made 30 yummy mini muffins.
I swapped cinnamon applesauce for the yogurt and made a combo of dark chocolate chips and peanut butter chips. I also did 1/4 c of oat flour and 3/4 AP flour in place of WW flour. They came out excellent. They have a great texture and are not too sweet. Thank you!
WOW!!!!! These are amazing. So moist and chocolatey, yummmmm. Here are the substitutions I used: I used zero sugar chobani vanilla yogurt, zero sugar maple syrup, coconut oil, unsweetened vanilla oat milk, and all purpose flour, and they came out so good. They taste like regular chocolate muffins, you would never know it doesn’t have any added sugar! You can def leave out the choc chips if you wanted it to be even more healthy 😊
Delicious! They taste so good. Very moist and yummy. I doubled the recipe and used extra yogurt instead of oil. I baked them for 20 minutes. Perfection! Will be making again.
This is our family’s go-to chocolate muffin recipe. Not only do we love the simple, clean ingredients, but the texture is perfect, sweetness level just right. Do not skip the espresso powder! Game changer in terms of rich, chocolately flavor. Thank you Erin!
Very chocolatey and not too sweet. Perfect for a muffin! Moist. I may try omitting the extra 2 T of flour. I used whole wheat flour, skim milk, maple syrup and vanilla Greek yogurt because that’s what I had. Skipped expresso powder because I didn’t have any. 🙃
I just made these for Sunday brunch and they turned out perfectly. The only changes I made were to use regular whole wheat flour, fat-free, lactose-free milk (FairLife for extra protein), and increased the cocoa to 1/2 cup because I wanted them extra chocolatey. What I love about these is that they’re not too sweet. (If you want them sweeter, you could always use milk chocolate chips rather than the semi-sweet). They were perfect with a glass of cold milk! Thanks for this yummy recipe, Erin!
We LOVE this recipe! It’s become a regular for us. I use whole spelt flour, non-dairy yogurt, olive oil and maple syrup as substitutes. Turns out great!
A fun tip if you have kids: Bake the entire recipe in a round cake pan (8 or 9 inch), but leave out the chocolate chips during baking. When it’s done, remove from the oven and top with the chocolate chips and smooth them around the top of the cake when melted, like frosting. It then seems like gooey, chocolate cake is for breakfast! 😉
We absolutely loved the muffins! They were awesome and I will make them again.
I used whole milk as that was what I had on hand. Substituted applesauce for canola oil. And used 1/4 cup honey and 1/4 maple syrup.
The batter did seem a bit runny so I added 3 additional tablespoons of flour. We live at 7000 ft elevation so that could be why. I did not make any of the other typical adjustments for elevation.
I made 18 smaller muffins instead of the 12 that the recipe suggested. Used silicon baking cups.
Also to freeze, after they were completely cool I put the muffins on a cookie sheet and put them in the freezer. When completely frozen (about 6-hours), I put the muffins in a ziplock bag then back in to the freezer.
I love your Well Plated Cookbook. My husband calls it my coffee table cookbook because I never put it away. So many excellent recipes. Thank you!
Great recipe! I’ve tried other healthy recipes and the texture has been off. This one has great flavor and is very moist. Will definitely keep this one!
Delicious! I added 4 tbsp chia seeds + more milk and coco powder. Also swapped choco chips with chopped nuts and a tiny bit of oats. Going to be making these weekly! Thank you for this wonderful recipe.
These are awesome! Made a few tweaks. I used wholemeal self raising flour, baking powder, whole milk, full fat greek yoghurt and used coconut oil. Such a great recipe. Cooked in 20 minutes. Probably the best muffins cupcake (whatever you want to call them) I’ve ever made. Both me and hubby very pleased. Thanks for this recipe!
I always substitute half the amount of flour with oats for more fibre. And I used 1/4 cup of coconut sugar and 1/4 cup of maple syrup. I added a whole grated apple for added sweetness. It worked beautifully. would make this recipe again.
Honey, especially high quality honey, has many health benefits. Honey is rich in antioxidants which can reduce cholesterol, lower blood pressure & triglycerides and reduce the risk of heart disease. It is also a much better alternative than refined sugar. Yes honey is high sugar and calories, but in moderation for a healthier sweet treat, why not? Chocolate also has health benefits, dark chocolate even more so. So you could use dark chocolate chips instead.
Hi Christine! Because these muffins are very moist, a lower temperature with a longer bake time ensures even cooking. They are also naturally sweetened, and natural sweeteners like honey caramelize very quickly in the oven, so I used a lower temperature to keep the muffins from becoming too dark. I hope you enjoy the recipe if you try it!
Delicious and moist, I used applesauce instead of yogurt and they came out great!
We LOVE this recipe! It’s become a regular for us. I use whole spelt flour, non-dairy yogurt, olive oil and maple syrup as substitutes. Turns out great!
A fun tip if you have kids: Bake the entire recipe in a round cake pan (8 or 9 inch), but leave out the chocolate chips during baking. When it’s done, remove from the oven and top with the chocolate chips and smooth them around the top of the cake when melted, like frosting. It then seems like gooey, chocolate cake is for breakfast! 😉
Yay! So glad the substitutions work for you J! Thanks for the tip!
Delicious! I added 4 tbsp chia seeds + more milk and coco powder. Also swapped choco chips with chopped nuts and a tiny bit of oats. Going to be making these weekly! Thank you for this wonderful recipe.
Yum! Thanks Grace!
This recipe was so good and I will defiantly be making this again. (I forgot to add extra chocolate chips) and so I wish there was a little more included in the recipe.
Happy to hear you enjoyed the muffins, Elizabeth! Thank you!
how many calories do you think each muffin has? they are delicious by the way!
Hi Abbe, one is roughly 193calories. The nutritional information is located at the bottom of the recipe. Hope this helps!
Great recipe! I’ve tried other healthy recipes and the texture has been off. This one has great flavor and is very moist. Will definitely keep this one!
So glad to hear you enjoyed the muffins, Lisa! Thank you!
Just made a batch of these and they are yummy. Loved the ingredients used!
Great to hear! Thank you Kaye!
I realized I didn’t have enough eggs so I used half a cup of unsweetened apple sauce instead. Worked like a charm! So that’s another way to veganize them too!
(Notes for anyone else trying—I didn’t use espesso powder and did use extra virgin olive oil instead of canola oil, don’t know if using espresso powder and canola oil would interfere with the apple sauce in any way)
Thanks for a delicious *and adaptable* recipe, Erin!
So glad they came out for you, Kyle! Thank you!
Could you use regular flour or all in one gluten free flour instead of whole wheat flour?
Hi Stephanie, yes! Anytime you see it written “white whole wheat flour” you can substitute with all-purpose flour or an 1:1 gluten free flour. Hope this helps!
Can I use Agave instead of honey or maple syrup? Thank you!
Hi Sarah, I haven’t tested it with agave but other readers have with success. Let us know how it goes if you decide to experiment!
I have made these twice now. The flavor is amazing, but they sink in the middle when I take them out of the oven.i used almond flour, would that make a difference?
Hi Judith, we’ve not tested these with almond flour but that is likely the cause. When using oat flour this is what we recommend and since it is interchangeable with almond flour I’d start here: “Swap one-fourth of the amount of white whole wheat flour with the same amount of oat flour.” Let us know how it goes!
I made these into mini muffins & swapped the chocolate chips for a chopped up dairy milk bar (1/2 of the chocolate called for) and they are SO delicious. Made 30 yummy mini muffins.
Yay! So glad to hear, Karly! Thank you!
I swapped cinnamon applesauce for the yogurt and made a combo of dark chocolate chips and peanut butter chips. I also did 1/4 c of oat flour and 3/4 AP flour in place of WW flour. They came out excellent. They have a great texture and are not too sweet. Thank you!
So glad to hear, Anna! Thank you!
Can this be made with almond flour for a lower carb version?
Hi Amy! Unfortunately you cannot swap almond flour for wheat flour. But you might love these almond flour muffins! https://www.wellplated.com/almond-flour-pumpkin-muffins/
WOW!!!!! These are amazing. So moist and chocolatey, yummmmm. Here are the substitutions I used: I used zero sugar chobani vanilla yogurt, zero sugar maple syrup, coconut oil, unsweetened vanilla oat milk, and all purpose flour, and they came out so good. They taste like regular chocolate muffins, you would never know it doesn’t have any added sugar! You can def leave out the choc chips if you wanted it to be even more healthy 😊
Glad it worked!
Delicious! They taste so good. Very moist and yummy. I doubled the recipe and used extra yogurt instead of oil. I baked them for 20 minutes. Perfection! Will be making again.
So glad to hear, Maddie Jo! Thank you!
This is our family’s go-to chocolate muffin recipe. Not only do we love the simple, clean ingredients, but the texture is perfect, sweetness level just right. Do not skip the espresso powder! Game changer in terms of rich, chocolately flavor. Thank you Erin!
Love to hear that! Thank you Sydney!
Very chocolatey and not too sweet. Perfect for a muffin! Moist. I may try omitting the extra 2 T of flour. I used whole wheat flour, skim milk, maple syrup and vanilla Greek yogurt because that’s what I had. Skipped expresso powder because I didn’t have any. 🙃
Very good recipe!
They look perfect, Dawn! So happy to hear you enjoyed the muffins!
I just made these for Sunday brunch and they turned out perfectly. The only changes I made were to use regular whole wheat flour, fat-free, lactose-free milk (FairLife for extra protein), and increased the cocoa to 1/2 cup because I wanted them extra chocolatey. What I love about these is that they’re not too sweet. (If you want them sweeter, you could always use milk chocolate chips rather than the semi-sweet). They were perfect with a glass of cold milk! Thanks for this yummy recipe, Erin!
They look fantastic, Tonya! Thank you for sharing!