Healthy Chocolate Muffins with Greek yogurt, applesauce, whole wheat flour, cacao powder and honey. Kids absolutely love these fudgy and nutritious muffins.
This muffin recipe is a delicious chocolate-y cross between my healthy chocolate bread and healthy chocolate cake.
Whole Wheat Chocolate Muffins
I had no plans to post these healthy chocolate muffins as I was preparing them for kids’ and Alex’s lunch boxes for the week. I guess I was wrong: 12 muffins were gone in 4 hours between 4 of us and in the morning kids were super upset none made to their lunch boxes.
They obviously love healthy chocolate chip muffins and these healthy chocolate chip cookies but never I expected such demand for these chocolate muffins with Greek yogurt and applesauce. I remade them yesterday and 5 muffins were gone still piping hot – my oldest one had a friend over and between 2 of them they ate 5 muffins. Seriously, what’s up with these muffins?!
These chocolate muffins are as good as chocolate bars and healthy chocolate ice cream! Indulgently fudgy, moist and chocolate chip loaded.
My word of advice when making these chocolate muffins. Make a double batch! You won’t regret it. At my house, these muffins are gone before they have even cooled down!
Ingredients for Healthy Chocolate Muffins
- Eggs: One time I ran out of eggs and used 1 large egg + 3 tbsp ground flaxseed soaked in 6 tbsp warm water for 10 mins. Which makes a vegan egg replacer. Very moist and fudgy results – try that.
- Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another.
- Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with powdered as it will offset liquid:dry ingredients ratio and recipe will not turn out.
- Cacao or cocoa powder
- Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again “baking is a science”.
- Baking essentials: Baking powder, baking soda, salt.
- Chocolate chips
How to Make Healthy Chocolate Muffins
There is a full recipe card below.
- Combine wet ingredients: First, whisk the eggs. Then add applesauce, yogurt and maple syrup and whisk to combine.
- Add dry ingredients: Add cacao powder, baking powder, baking soda and salt. Whisk thoroughly until smooth and no lumps. This step eliminates the need for 2 bowls with dry and wet ingredients, just like it works with chocolate zucchini bread. It does work if you mix well!
You will see the chocolate mixture rising and bubbling due to the chemical reaction between the acid in the applesauce and baking soda. Don’t worry!
- Add flour: Gently mix with spatula just enough to combine. Do not over mix, let batter sit for a few seconds, then stir again. Add chocolate chips and give a few gentle stirs to incorporate.
- Bake for 25 minutes: Distribute batter evenly between 12 openings of a muffin tin. Bake at 350 degrees on the third or fourth rack from the bottom (farther away from heat). This way the muffins will rise slower, forming a nice dome.
Storing and Freezing
Storing: Muffins stay fresh for up to one week in the fridge. The way these whole wheat chocolate muffins disappear in my house, I always bake a double batch. Always!
Freezing: If you make a double batch (or if you have any leftover muffins), you can always freeze these little breads. They will last for up to 3 months in any air tight container.
More Healthy Chocolate Recipes
- Chocolate quinoa muffins
- Chocolate coconut flour muffins
- Chocolate coconut balls
- Chocolate chia pudding
- Coconut oil fudge
Healthy Chocolate Muffins
Ingredients
- 2 large eggs
- 1 cup applesauce unsweetened
- 1/2 cup Greek or regular 2%+ fat yogurt, plain
- 1/2 cup + 2 tbsp maple syrup or honey
- 1/3 cup cacao or cocoa powder
- 2 tsp baking powder aluminum free
- 1 tsp baking soda
- 1/4 tsp salt
- 1 3/4 cups whole wheat or spelt flour
- 1/2 cup chocolate chips
- Cooking spray I use Misto
Instructions
- Preheat oven to 350 degrees F and spray silicone muffin tin with cooking spray. Set aside.
- In a medium mixing bowl, whisk eggs for 15 seconds. Add applesauce, yogurt, maple syrup and whisk to combine. Add cacao powder, baking powder, baking soda, and salt; whisk thoroughly until smooth and no lumps.
- Add flour and gently mix with spatula just enough to combine. Do not over mix, let batter sit for a few seconds, then stir again. Add chocolate chips and give a few gentle stirs to incorporate.
- Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop) and bake on a third-fourth rack from the bottom (farther away from heat) for 25 minutes or until a toothpick inserted in the centre comes out clean.
- Let muffins cool for about 5 minutes and transfer to a cooling rack to cool off completely.
Store: Refrigerate in an airtight container for up to 1 week or freeze for up to 3 months.
Notes
- Applesauce and Greek yogurt: You do need to use both and one cannot be substituted for another.
- Maple syrup or honey: Baking is a science and unfortunately you can’t substitute wet sweetener with powdered as it will offset liquid:dry ingredients ratio and recipe will not turn out.
- Whole wheat flour or spelt flour: Chocolate muffin recipe will not work with any other flour because again "baking is a science".
- Egg replacement: One time I ran out of eggs and used 1 large egg + 3 tbsp ground flaxseed soaked in 6 tbsp warm water for 10 mins. Which makes a vegan egg replacer. Very moist and fudgy results - try that.
Nutrition
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Hi! I can’t wait to try these! I only have metal muffin tins, not silicone… Will that be a problem? (I’m new to baking!) 🙂
~Morgan
No problem at all. Spray it well with cooking spray or use parchment paper liners sprayed with cooking spray. Enjoy!
I messed up at added too much baking soda. So I doubled the batch – so glad I did! These are amazing. I don’t know if my double batch will make it to the freezer. Another amazing recipe.
Haha, these are very very good as per my kids. I’m so glad you enjoyed it, Melissa! Thank you for the wonderful review!
Hi we love these choc muffins.Thank you for the recipe.
You’re welcome June!
These were deliciously fudgy and moist!
I haven’t made these yet but several people mentioned “drizzle” in their reviews and I can’t find the directions for it in the recipe! I’m VERY interested and have spent a long time looking for these directions, through other muffin recipes, etc and simply can NOT find them! Please put them somewhere easy to find as I’m just crazy to try this recipe WITH the drizzle! Thank you so much and I just love all your recipes!
Sorry made you look that long. 🙂 It used to be on older recipe. All it is just melted chocolate chips with a bit of coconut oil to melt and then drizzle and it will set.
Hi Olena,
Can I use white flour as I don’t have whole wheat on hand ??
You might. I have not tried though. General recommendation is to use 1 cup of white flour for every 3/4 cup of whole wheat flour that recipe calls for.
Another great keeper recipe, simply awesome. I replaced half cup of whole wheat flour with almond flour and added some finely chopped walnuts along with the chocolate chips and didn’t add the 2tbsp maple syrup. The muffin turned out pillowy soft and mildly sweet just like the way we like it in our home. And I totally agree with you on how the north American kids’s diet is out of control and loaded with sugar. With our authority as a parent we can definitely change that. Anyway thanks for the great recipe.
You are very welcome Nidhya!
Hi! Olena!
Would substituting mashed bananas instead of applesauce be ok?
Looking forward to another delicious creation! (I need to use up my ripe bananas. )
Hi Lisa. Yes, I am pretty sure it will work. Enjoy!
They were great! Best ever, changing the applesauce for mashed bananas worked out well!
Awesome!!! Happy to hear, Lisa!
I’ve been making these for years, finally leaving a review:). Fantastic recipe, my whole family loves these.
So happy you finally let me know. Awesome!
Love chocolate muffins …thank you for this amaaazing recipe.
Is it ok to use almond flour for this recipe ?
Unfortunately not. Won’t work. Try my almond flour banana muffins.
Tried them already and I’m in loooove ? my sister and I just made two batches today as well.
However, my brother is a huge fan of banana flavor… any advice on how to make the banana flavor more intense ?
Add banana extract.:) Maybe there is a natural one! Or add crushed banana chips, they are already flavored.
Oh my goodness my daughter and grandson love them!!
That’s amazing!
This was a great recipe. I have been trying out different chocolate muffin recipes and this is the best I have tried. Only change I made was using flax eggs instead of regular.
Yummy I used honey and dark chocolate cocoa powder. Mil didn’t not to sweet. perfect
Sounds great, Mary! So happy you enjoyed my healthy chocolate muffins.:)
Another delicious recipe Olena. I find I usually end up back on your website when I want something sweet and healthy that is straightforward to make. I only had raw cacao nibs on hand which are kind of bitter so added a couple of tablespoons of homemade strawberry jam to compensate. Delicious!
Yay! So happy to hear my healthy chocolate muffins were a hit with you. Smart move – you must have Ukrainian in you! No need to waste gas and time on store trips, right?! Yes, cacao nibs are bitter.
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!
Hi Sarah! Good!!! Re: calories. I finally got over the fear of too many calories. As long as I am eating healthy who cares about calories? Seriously?! If I don’t eat extra calories in this chocolate muffin, I will catch up on them somewhere else – my body knows better how many calories I need by sending hunger cues to my brain. Duuuh. And even when you treat yourself to fries or pizza, whatever, as long as we eat healthy majority of time. Our body is not a calculator. Unless you want to compete in a fitness competition of course which makes you a super brave person lol. So enjoy!!!
So true! Nope, definitely not doing a fitness competition. LOL. I’m on the mindset of eating healthy calories and not empty calories! I’m a breastfeeding mama too so I know I definitely need them! Looking forward to making more of your recipes!
Exactly! I remember I was SO hungry and thirsty breastfeeding, so eat it up. Enjoy and please leave me a comment the ones you try.
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
Mmmm…I don’t even have kids yet, and these would devoured so fast between just the hubby and me! These look absolutely amazing and delish! 🙂 Pinned!
Deliciousness! Just made these. Happiness is…..
Love your site. Thanks for all these amazing recipes 🙂
Thank you and enjoy! 🙂
Hi Olena! Any substitutes for the greek yogurt? I’m out!
Maybe more applesauce?! I haven’t tried though.
Hello! Have you tried these as a bread, or have suggestions for doing so?
Thanks,
Natasha
I’m sure it should work just increase baking time to like 50-60 minutes.
I love chocolate muffins. This one’s sound and looks good. I have to give this a try! Pinned.
Chocolate muffins are a win win in my book. I like to make my own “sweets” for my kids too. I was super excited when I saw this post. These will have to wait until after love day. I’ve got everything ready for that whole berry coffee cake you posted for tomorrow. 🙂
I hope you liked it.:) I never buy ️muffins!
I saw your newsletter in my inbox this morning with this recipe and knew I had to make them right away for a valentine’s treat for the kids. And me 🙂
Haha. I know it might sound a bit insane to have muffins for Valentine’s but these are so indulgent…Sometimes simple is best. Most times. Enjoy!:) I think I will end up with another dessert experiment on my Valentine’s Day.
Just made these, they’re excellent! Super moist and perfect for my chocolate craving!
Wow, you are fast! OK, so it’s not only us LOL. Enjoy! I need to restock on cacao powder and make them again.
Wow – I don’t blame y’all – we would have finished them in 4 hours too -but we are a house of 2!!! These sound delicious!
It wouldn’t be hard.:)
Oh yum those look delicious! I would totally go for chocolate for breakfast 🙂