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.
Healthy Chocolate Muffins stacked on a plate with a bite taken out of one, showing the inside muffin crumb..

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).

Three process photos for making the batter for chocolate muffins, in a mixing bowl.

  • 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.

Chocolate muffin batter in a muffin tin next to another photo of the baked muffins on a plate.

Freezing Instructions: Allow muffins to cool completely. Store them in a freezer-safe ziplock bag or air-tight container.

Consider trying healthy snacks:

Skinny Banana Bread Muffins

Energy Bites

Easy Homemade Applesauce

Healthy Granola

Healthy Frozen Yogurt

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Recipe

Healthy Chocolate Muffins stacked on a plate with a bite taken out of one.
Prep 10 minutes
Cook 15 minutes
Total 25 minutes
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Ingredients
  

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

Freezing Instructions: Allow muffins to cool completely. Store them in a freezer-safe ziplock bag or air-tight container.

Nutrition

Calories: 153kcalCarbohydrates: 23gProtein: 5gFat: 5gSaturated Fat: 3gCholesterol: 33mgSodium: 162mgPotassium: 147mgFiber: 2gSugar: 11gVitamin A: 65IUCalcium: 39mgIron: 2mg

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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.

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About The Author

Lauren Allen

Welcome! I’m Lauren, a mom of four and lover of good food. Here you’ll find easy recipes and weeknight meal ideas made with real ingredients, with step-by-step photos and videos.

4.1 8 votes
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4.94 from 130 votes (95 ratings without comment)
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Arham
3 years ago

4 stars
They were tasty but if you omit the chocolate chips be sure to add more sugar otherwise they will be a bit bland.

Alice
3 years ago

5 stars
These have been my go to chocolate chip muffins ever since I first stumbled across this recipe! They are so delicious & my family is always satisfied 😊

Elaine
3 years ago

5 stars
I used fresh mashed bananas, non fat Greek yogurt and low fat milk and it turned out amazing! Also I baked them in an air fryer.
If you like low fat and not too sweet dessert, you should definitely try this recipe.

Dianne
3 years ago

Can I use granulated monkfruit instead of sugar?

Admin
3 years ago
Reply to  Dianne

We haven’t tested that but it will probably work. You may want to look into the conversation from monk fruit to sugar as I think monk fruit is sweeter.

Tam
3 years ago

Can Unsweetened Almond milk be used? If Greek yogurt is used, am I using fat-free? Would this be the same for the sour cream?

Admin
3 years ago
Reply to  Tam

Almond milk is fine! You can use any kind of Greek Yogurt or sour cream (I usually use fat-free!)! Let us know what you think!

Shannon
3 years ago

These turned out amazing with a few changes I made. I omitted the granulated sugar and instead used 4.5 tablespoons of maple syrup and an additional 1/12 of a teaspoon of baking soda. I also used melted Crisco (because that’s what I had on hand) instead of applesauce, oil, or banana. Be sure to wait a few minutes before adding your melted oil to the liquid mixture. And replaced the whole wheat flour with almond flour. I cut down the milk from 1/2 cup to 5 tablespoons to account for the additional liquid in the recipe from the maple syrup. I also added walnuts.

I encourage other bakers to experiment with what you have. The internet is full of answers to questions you’re probably asking yourself trying to solve a baking problem. It’s never been easier to replace butter, oil, sugar, etc in a recipe! Every article about that has already been written for you! The internet is your best resource, take advantage of it.

SueG
2 years ago
Reply to  Shannon

“Experiment with what you have” applies to cooking, not usually baking. Unless it’s an optional ingredient like swapping raisins for chocolate chips you could be messing with the delicate balance of science to make the correct magic happen in your baked good. As you see from another commenter who took your advice, it was a complete fail for her. It depends what type of ingredient you are subbing for and a lot of inexperienced bakers will not to well with this. I’ve been cooking for 25 years and never bake b/c I strictly “use what I have”. I need flexibility but when baking it’s pretty much by the book which is why I don’t do it often. I think it’s good advice to be prepared and have all the ingredients you need ready beforehand if you’re going to spend the time & money to bake something. Ingredients can be expensive and there is nothing more disheartening than having your efforts be for naught, wasting your afternoon only to throw something you looked forward to away. Novices should know what subs are appropriate or follow a baking recipe 1st before they start tweaking it.

Shannon
3 years ago

I’ll be making these with maple syrup instead of granulated sugar, adding walnuts, and using almond flour instead of whole wheat. I’ll be sure to update y’all on how they turned out tomorrow after baking them! Thanks for the recipe!

Zach
4 years ago

3 stars
I made them and they turned out to have little flavor. Not sure if I did anything wrong. Could have been too much apple sauce for one.

Jenn
4 years ago

5 stars
I made them per the recipe, using nonfat greek yogurt, almond milk, unsweetened applesauce (it didn’t specify but I only keep unsweetened) and 2/3 cup full size chocolate chips plus some for sprinkling before baking. Very good! Will make these again since I keep all the ingredients on hand.

Stephanie
4 years ago

Made it with cacoa nibs instead of chocolate chips. So delicious!