These Healthy Chocolate Muffins are indulgently fudgy, fluffy and moist. Made with whole grains, no oil, naturally sweetened and loaded with chocolate chips.
Reader’s Review
I made these muffins for the 1st time at weekend, oh boy! What a hit they were too, so soft, moist and so tasty! Will definitely be a regular bake in this house.
Julie
Why You’ll Love These Muffins
I used the batter from these healthy chocolate muffins to make Dubai chocolate muffins and was instantly reminded how good they are! And then I read the comments and I see you guys are in love with them too!
They taste so indulgent but in fact are a true definition of a healthy muffin! No oil, refined sugar (except in the chocolate chips), naturally sweetened with maple syrup, and moistened with yogurt and applesauce.
The addition of Greek yogurt not only helps with moisture but the bonus is that it provides protein. I use whole wheat flour or spelt flour which is a more wholesome choice for this healthy chocolate muffin recipe!
Ingredients for Healthy Chocolate Muffins
- Cacao or cocoa powder: Use whichever you’d like. From a health standpoint, cacao powder is less processed, but unsweetened cocoa powder still has a ton of benefits.
- Whole wheat flour: I like to use whole wheat flour or spelt flour. I think white whole wheat flour or whole wheat pastry flour will work 1:1 ratio.
- Applesauce and yogurt: You do need to use both and one cannot be substituted for another. Although applesauce provides a bit of sweetness as is, I opt for unsweetened applesauce to keep it refined sugar free. Greek or regular yogurt works.
- Eggs: Used for binding and texture.
- Maple syrup: You can use any other liquid sweetener you like. Examples would be honey, agave, sugar-free syrup etc.
- Baking essentials: Baking powder, baking soda and salt.
- Chocolate chips: I often use mini chocolate chips so I get more chocolate in each bite but regular size works too. I use semi-sweet chocolate chips because I find they’re the perfect balance of not too sweet, not too bitter but if you prefer dark chocolate, by all means, use dark chocolate chips instead.
Substitutions
- All-purpose flour: I do have a conversion chart that I often use in baking. I have not tried all-purpose flour in this specific chocolate muffin recipe but if I were to, I would use 2 1/4 cups of all-purpose flour.
- Gluten-free flour: Gluten-free flour can get a little complicated. It’s not always a 1:1 substitution. Your best-case scenario is to use Bob’s Red Mill gluten-free baking blend and use above mentioned 2 1/4 cups white flour sub measurements. I haven’t tried oat flour or almond flour.
- Mashed banana instead of applesauce: Ripe bananas will provide an incredible sweetness with an element of banana flavor which always pairs well with chocolate. Use same amount as applesauce.
- Egg-free: You can try an egg replacer or flax eggs or chia eggs.
How to Make Healthy Chocolate Muffins
A muffin tin holds 12 muffins but this recipe makes enough batter for 15 muffins. You can either use 2 muffin pans or bake in batches.
Preheat oven to 325 degrees. Grab a muffin pan and place muffin liners into each cup. Spray with cooking spray (I use Misto). Set it aside.
- “Bloom” the cacao powder: In a large mixing bowl, whisk boiling water and cacao powder. This will help to gain that rich chocolate flavor.
- Add wet ingredients: Whisk in the applesauce and yogurt followed by the eggs and maple syrup. Mix to combine and set aside.
- Combine dry ingredients: Mix the flour, baking powder, baking soda, and salt. Whisk until smooth and lump-free.
- Add dry to wet ingredients: Add the flour mixture to the chocolate mixture, stir gently and let batter sit for a minute, then stir again. Do not overmix.
- Add chocolate chips: Add 1/2 cup of chocolate chips and fold them in a few times making sure they’re evenly distributed.
- Bake and cool: Fill each muffin opening 2/3 full with batter and sprinkle with remaining 1/4 cup of chocolate chips. Bake on a middle rack for 22 minutes. You’ll know your muffins are done when you insert a toothpick into the center and it comes out clean. Let your muffins cool in the tin for 5 minutes before placing on a wire rack to continue cooling.
Additions and Variations
- Dried fruit: Chocolate and cherries are always a great pairing! Add up to 1/2 cup. Cranberries perhaps, or dried mango or coconut.
- Nuts: Add up to 1/3 cup of chopped walnuts, pistachios, pecans, almonds, you name it.
- Espresso or instant coffee: It enhances the chocolate flavor without making anything taste like coffee.
- Cacao nibs with strawberry jam: Yum! You could use whatever flavor of jam you want.
- Add a drizzle: Let’s turn this into a triple chocolate muffin! Melt chocolate chips with a bit of coconut oil to melt, then drizzle on top and wait for it to set.
- Added flavor: A dash of cinnamon or a couple drops of vanilla extract would be delicious especially during the cooler months.
How to Store
Store: Healthy chocolate muffins stay fresh for up to 3-4 days in a cool dry place. The way these muffins disappear in my house, I always bake a double batch. Always!
Freeze: If you make a double batch (or if you have any leftover muffins), you can always keep them in the freezer. They will last for up to 3 months in an airtight container.
Storage Tip
For more muffin storage practices, check out my posts how to store muffins and how to freeze muffins.
More Healthy Chocolate Recipes
- Chocolate veggie muffins
- Healthy chocolate zucchini bread
- Healthy chocolate chip muffins
- Chocolate coconut flour muffins
- Chocolate quinoa muffins
- Chocolate zucchini muffins
- Healthy chocolate bread
Healthy Chocolate Muffins
Equipment
Ingredients
- 1/2 cup cacao or cocoa powder
- 1/2 cup boiling water
- 3/4 cup applesauce, unsweetened
- 1/2 cup plain Greek or regular yogurt, 2%+ fat
- 2 large eggs
- 3/4 cup maple syrup or honey
- 1 1/2 teaspoons baking powder, aluminum free
- 1 teaspoon baking soda
- 1/4 teaspoon salt
- 1 3/4 cups+ 3 tablespoons whole wheat or spelt flour
- 3/4 cup chocolate chips, divided
- Cooking spray, I use Misto
Instructions
- Preheat oven to 325 degrees F, line muffin tin with liners and spray with cooking spray. This recipe makes 15 muffins or so, so either bake in 2 tins or 2 batches. Set aside.
- In a large bowl, add cacao powder and boiling water; whisk until smooth. Add applesauce and yogurt; whisk. Now add eggs and maple syrup; whisk until smooth. Set aside.
- In a medium bowl, combine flour, baking powder, baking soda and salt. Whisk until no lumps, add to the bowl with chocolate mixture and gently mix with a spatula just enough to combine. Do not over mix, let batter sit for a few minutes, then stir again. Add 1/2 cup chocolate chips and give a few gentle stirs to incorporate.
- Fill each opening 2/3 batter full and sprinkle remaining 1/4 cup of chocolate chips on top (this recipe makes 15 muffins or so, so either bake in 2 tins or 2 batches). Bake on a middle rack for 22 minutes or until a toothpick inserted in the centre comes out clean.
- Remove from the oven, let muffins cool for about 5 minutes and transfer to a cooling rack to cool off a bit more.
Notes
- Store: In a cool dry place covered for 3-4 days.
- Freeze: In an airtight container up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
The best healthy chocolate muffins I ever tried and I have tried a few! THANK YOU!
These were absolutely DELICIOUS! I loved these and so did my husband. He wouldn’t stop eating them. Same with my kids. They would be all gone in one day!
Hi Olena!
I just pulled these out of the oven, they turned out fantastic. I did not have applesauce so I used 1/2 cup coconut oil, and upped the greek yogurt to 1 cup. I know… more calories… but still nutritious! Thank a ton for the recipe!
Oh my! What a delicious treat! I absolutely loved the way these turned out. The drizzle is a must. Thanks for the great recipe. I’ll be making them again for sure!
You are welcome, Christina! These whole wheat chocolate muffins and banana muffins I make over and over again.
I can’t wait to try these! Are the nutrition facts figured up with or without the chocolate drizzle??
Without.:) Let me know how you like them, Heather.
These are amazing. I just made them! I used paper baking cups and they stuck pretty good. We didnt mind they were so good. Thank you!
Yay! Spray paper cups with cooking spray well next time. Because all my healthy muffins do not contain much oil I either use silicone muffin tin, cooking spray or parchment paper cups. Never stick. And the key is to let muffins cool down almost completely (silicone tray needs less cooling time). I used paper cups from $ store before and everything sticks to them.
These are amazing! My son is a very picky eater and would request 2-3 of the for breakfast! Thanks for sharing! Do you think this recipe would work as a basic muffin recipe (minus the coco powder) to add other “fillings” and “toppings” to? They were just the best whole wheat recipe I have tried so far.
Hi Andrea. Glad to hear that.:) If you are kind of good with baking yes you could do that. However, because you are removing cacao powder it might be too much honey. If you reduce honey, you might need to add a tad bit less flour or maybe not. Just keep that in mind. You might also like these Blueberry Muffins. Easy with any toppings.
Wow! Love love these, I just made these muffins for my husband’s co-workers and they LOVED THEM! They asked my husband what else I could make for them. So now they want more muffins which is great. I love to make them. Thanks for sharing this recipe.
You are welcome, Amy!
I made this for my company potluck today. I used oat flour because that is all I had on hand. It was so good and a hit at work. Thanks again for another yummy clean treat.
Wow. And they rose nicely with oat flour?
Oh my gosh, these are A-MA-ZING!!!! Instead of all that flour, I used only half a cup and the rest was chocolate protein powder… so so good. Thank you for this recipe!!! <3
Yay! Did you use whey or plant based protein powder?
I used whey, a combo of Cellucor and Shakeology