This post contains affiliate links.
These healthy Chocolate Muffins are DELICIOUS and completely guilt-free, made with whole grains and only 150 calories each!
Just like so many of my other favorite muffin recipes, these freeze wonderfully for an easy and quick breakfast or snack.

These skinny chocolate muffins are way healthier than any store bought chocolate muffin but they still have the same great flavor and texture. I call that a major WIN!
How to make Healthy Chocolate Muffins:
- Preheat oven to 350 degrees F. Grease a standard 12 cup muffin tin with non-stick cooking spray.
- In a large bowl, combine the dry ingredients: flours, sugar, cocoa, baking soda, cinnamon, salt and chocolate chips and stir to combine.
- In a medium bowl, beat together the eggs, yogurt, milk, applesauce and vanilla. Make a well in the center of the dry ingredients and stir in the wet mixture, stirring just until moistened (don't over-mix).

- Divide batter between muffin cups. Bake for 12-15 minutes or until a toothpick inserted in the center comes out clean. Remove to a wire rack to cool completely.

Freezing Instructions: Allow muffins to cool completely. Store them in a freezer-safe ziplock bag or air-tight container.
Consider trying healthy snacks:
FOLLOW ME on FACEBOOK, TWITTER, INSTAGRAM and PINTEREST for more great recipes!

Skinny Chocolate Muffins
Ingredients
- 1/2 cup whole wheat flour
- 2/3 cup all-purpose flour
- 1/3 cup granulated sugar
- 1/3 cup unsweetened cocoa powder
- 1 teaspoon baking soda
- 1/4 teaspoon ground cinnamon
- 1/4 teaspoon salt
- 1/2 cup mini semi-sweet chocolate chips
- 2 large eggs
- 1/2 cup Greek yogurt, or sour cream
- 1/2 cup milk
- 1/4 cup applesauce, , oil or a mashed banana
- 1 teaspoon vanilla extract
Instructions
- Preheat oven to 350 degrees F. Grease a standard 12 cup muffin tin with non-stick cooking spray.
- In a large bowl, combine the dry ingredients: flours, sugar, cocoa, baking soda, cinnamon, salt and chocolate chips and stir to combine.
- In a medium bowl, beat together the eggs, yogurt, milk, applesauce and vanilla. Make a well in the center of the dry ingredients and stir in the wet mixture, stirring just until moistened (don't over-mix).
- Divide batter between muffin cups. Bake for 12-15 minutes or until a toothpick inserted in the center comes out clean. Remove to a wire rack to cool completely.
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Text me new recipe ideas!
Simple, tasty ideas sent once a week. No spam.
Check out my webstory.
Have you tried this recipe?!
RATE and COMMENT below! I would love to hear your experience.
I originally shared this recipe September 2017. Updated January 2020.



I did several mods. I used coconut flour and almond flour instead of the prescribed flours. I cut the sugar qty down to 1/4c, and to make up for loss of sweetness, I added 10 drops of liquid stevia. Also to help with sweetness, I added a 1/4 cup of chocolate pea protein powder (sweetened with stevia) and omitted both tablespoons in the flour amounts. I added 1tb spoon extra of milk (i used cashew milk in my recipe). I used Ghirardelli chocolate chips and my Greek yogurt brand was Fage. I think it ended up taking 20 mins in the oven. Came out great! Moist! Would make again!
Would it be too sugared if i use vanilla greek yogurt?
That would be fine.
I made these muffins a few times already into mini muffins and baked for 12 minutes. I added extra chocolate chips and a tablespoon of flaxseed meal. My daughter loves them! Great fast breakfast for a family on the go! They also freeze really well 🙂
I added a scoop of chocolate protein powder to this. Needed to add a touch more Greek yogurt and milk to keep the moisture up, but it turned out amazing. Adds roughly 2-3 grams of protein per muffin!
Fantastic recipe – this is a definite make-again.
Great idea! Thanks for sharing.
I just baked these yummy chocolate chip muffins. They are very tasty, moist, and very chocolatetey. I added an extra 1/4 cup of chocolate chips like many others who commented. When I added the 1/2 cup sugar, it was a combination of granulated and raw sugar. I’d love to stay away from granulated whenever I can make a better substitution. Great recipe. (In case my name throws you, I’m female.)
This sounds lovely! Could I use only whole wheat flour instead of half and half?
You can– they just may be a little denser 🙂
Hello Lauren, I just finished baking a batch of these muffins…
delicious! I added an extra 1/4 cup of chocolate chips (dedicated choclaholic). Thanks for the recipe! Val
Hello Lauren! I just finished baking your muffin recipe. Delicious! I made two tiny tweaks: added 1/4C extra chocolate chips (dedicated choclaholic) and 1/4C milk. Thanks for sharing your recipe! Val
I’m 10 years old and I absolutely love to bake. I made the muffins and enjoyed making them. I also loved eating them they turned out super moist. Thank you so much!
Reese, good job! I know your comment is 2 years old, but I absolutely LOVE to see young kiddos learning to cook/bake. I hope in the last 2 years you have become more proficient. I’m proud of you!!
My kids loved them. These will be one of the staple muffin snacks in my home now. Thanks!