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.
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.
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
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Coat your muffin tin with nonstick spray or line with paper liners.
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In a large bowl, whisk together the dry ingredients, and stir in the chocolate chips.
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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!
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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:
- 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.
- Eggs. If you’re creating a brunch spread, serve these muffins with a scrumptious egg recipe like this Crockpot Egg Casserole, Ham Sweet Potato Frittata, or Healthy Breakfast Egg Muffins.
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
- Healthy Zucchini Muffins with Chocolate Chips
- Chocolate Chunk Coffee Muffins
- Peanut Butter Muffins with Chocolate Chips
- Gluten Free Muffins
- Healthy Banana Muffins
Recommended Tools to Make Healthy Chocolate Muffins
- Standard muffin pan (I also like this option if you don’t need the lid)
- Batter scoop (my secret to big, puffy muffin tops)
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
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Ingredients
- 1 cup white whole wheat flour plus 2 tablespoons
- ⅓ cup unsweetened cocoa powder
- ¾ teaspoon baking soda
- ¾ teaspoon instant espresso powder optional; will result in a more intensely chocolaty muffin
- ¼ teaspoon kosher salt
- ⅛ teaspoon ground cinnamon
- ½ cup semi-sweet chocolate chips plus optional additional for sprinkling on top
- 2 large eggs at room temperature
- ½ cup nonfat plain Greek yogurt at room temperature
- ½ cup honey or pure maple syrup
- ⅓ cup unsweetened almond milk or milk of choice
- ¼ cup canola oil or melted, cooled coconut oil, light extra virgin olive oil, or melted, cooled unsalted butter
- 1 teaspoon pure vanilla extract
Instructions
- 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.
- For more storage tips, check out my post on How to Store Muffins and Other Quick Breads.
Nutrition
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Gave u to many stars before again if I wanted cupcakes I would have looked up cupcakes not muffins
I’m sorry to hear the recipe wasn’t to your liking, Lisa. As stated in the beginning of the blog post these muffins are brownie-like, so not your standard coffee shop muffin. The amounts, flavorings and timing have worked well for myself (and others) so I wished it would have been a hit for you too! I know it can be so disappointing to try a new recipe and it does not turn out for you.
The flavor was good, but the cooking temp and cooking time were not accurate for me at all. They ended up being in the oven over 45 minutes and for the last ten minutes I had to bump the temp up to 375. I was worried when the batter was so wet… I added an extra 1/3c of flour and it was still extremely wet.
Once they were finally cooked, they were delicious, but just a lot of issues getting them thoroughly cooked.
I’m sorry to hear you had trouble with the recipe, Macy but glad you were still able to enjoy them. I would refrain from adding more flour to them, as that was not intended with the original recipe, so not sure how that would affect the baking time. Also all ovens are different so mine must just run hotter than yours.
Best healthy chocolate muffins ever! My 2 year old devours these and there is no guilt. This recipe is being made on repeat.
Yay! Love that Meghan!
This was a good recipe! I subbed plain yogurt for Greek yogurt and dark chocolate chips for the semi-sweet. I baked the muffins for 5 minutes longer than the recipe stated. They were very good, will make again :)
So glad to hear, thank you Ali!
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.
So glad to hear, thank you Sylvia!
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!
Glad the substitutions are working for you, Rebecca! Thank you!
The family have given these muffins their thumbs up!! Absolutely delicious and so super moist. We are chocolate lovers so this reciepe is perfect, only adjustment we made was using dark chocolate chips.
My muffins did fall, but I suspect it was because I didn’t take them out of the hot muffin tin early enough to cool after baking (as we were eating dinner at the time). This reciepe will definitely be made on repeat!
So glad to hear you enjoyed them, Tarryn! Thank you!
Fantastic recipe! The sweetness level was perfect. Not too sweet at all, but still satisfies the chocolate craving. Thank you for sharing this!
So glad you enjoyed it, Monica! Thank you!
These turned out so well! My kiddos loved them.
I substituted regular yogurt for the Greek Yogurt and instead of adding the 2 tablespoons of white whole wheat flour, I used bread flour instead (just for the 2 tablespoons.) I love that this uses honey and whole wheat flour. I think I’ll be coming back to this recipe again and again.
Glad it worked for you, Rebeckah!
Recipe was easy and turned out wonderfully – loved by both my four and seven-year olds. My batter had a good consistency (almost like a thick pancake batter) and took between 18-20 min at 325 using mini muffin pans. My husband also loved the muffins and asked for me to add it to our recipe box where only our “keeper” recipes go.
So glad to hear! Thank you Heather!
Great recipe! My kids thought they were great, my son says they taste like brownie cupcakes! I kept them in the oven for an extra 5. Thank you for the recipe 🥰
So glad to hear, thank you Katie!
Hi, I had a question. I was wondering if I could sub the whole wheat flour for oat flour to make it gluten free? Or would the resulting bake be too dry? I was also wondering if you thought adding a 1/4 cup of nut butter would be alright? I am hoping to slightly increase the protein value for my grandmother who has dementia, she likes sweets and I want to make sure she’s eating enough fiber and protein.
Hi Jessie, I actually haven’t tried either of these substitutions so it would be hard for me to say for sure how it will turn out. I checked the comments and didn’t get any feedback from any other readers either. So it would be something you’d have to experiment with. If you decide to, let us know how it goes. Also check out our high protein recipes, you’d might find something there that fits the bill! https://www.wellplated.com/category/recipes-by-diet/high-protein/ Hope this helps!
I made this today & think it is delicious. I used wholemeal flour (it is more common in my country), full cream milk, plain greek yogurt, melted butter & dark chocolate chips. I made 12 servings as suggested in the recipe but i might increase the serving size for each muffin the next time i bake this as i want it to be big & full. The only issue i had was the bottom of the muffin sticks too much to the liner (i use baking paper). I’m not really sure what is the reason. Did i overbake the muffins? I baked the muffins at 425° for 5 minutes & 350° for 17 minutes. Total baking time was 22 minutes.
So glad to hear you enjoyed them, Jiha. Not sure why it sticks to the liners, maybe try a different liner or spray it ( I know not idea but it might work). Hope this helps!
It was amazing definitely 100% going to make them again
Great to hear, Caitlin! Thank you!
These are delicious! I have made them before and they fell so this time I decided to bake them at 400 degrees for five minutes and then without taking them out lower the temperature to 325 and bake for 10 more minutes. They were perfectly high and moist! I also added four tbsp of chocolate collagen powder so I upped the milk too
So glad to hear! Thanks for the feedback, Mary!
Great. Recipe but wondering how can I make them more moist also how do you prevent the mixture sticking to paper cup when cooked? . Wonder if I overcooked as they weren’t ready at all at 22 mins so left another ten mins but not sure what the perfect time was then
I used dates to add extra sweetness instead of choc chips and half oat flour to boost fiber content and added baking powder which helped them rise more
Hi Natasha, I’ve not had this issue with the written recipe, also I like using parchment paper liners. They are the best! Also the changes made to the recipe will change the end result.