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
  

  • 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

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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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.

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Comments

  1. 5 stars
    Came out great! I used paper liners and didn’t oil them, they did stick a bit but it’s expected. Followed recipe as is! I love that these don’t leave you with that sick to your stomach too sweet feeling. I might double the cinnamon next time as I do love a prominent cinnamon after taste. It doesn’t need it though!

    Any chance you could post the metric measurements or a conversion tool?

  2. 5 stars
    Very yummy, especially for how healthy it is. I used brown sugar instead of granulated, and almond flour instead of whole wheat but otherwise, I didn’t make any swaps. These would be delicious with a cup of milk 😋

  3. 5 stars
    Very tasty, easy, and quick. But first try was a flop. I will keep working on it to get it right. Easy recipe, but I’m new to baking and didn’t follow the recipe exactly .
    I tied to use homemade oat flour instead of whole wheat flour (ratio of 1.42 x Whole wheat flour).
    My muffins are yummy and moist but after I took them out of the oven (clean toothpick), the centers collapsed. I might have overfilled the cups. I also didn’t grease my silicon baking cups. Any other suggestions? Thanks!

    Looking forward to trying more of your recipes.

  4. 5 stars
    Absolutely fabulous recipe, giving the most delicious, very chocolate-y muffins ever! This is a keeper!!! Thanks so much! 🥰

  5. 5 stars
    So good! I made it gluten free and it worked perfectly: 1/2 C cassava, 1/3 C oat flour, 1/3 C almond flour.

  6. 5 stars
    Such yummy muffins!! I used coconut sugar instead of regular sugar and added in a tablespoon of melted cacao butter and they turned out delicious! Thank you so much for this recipe!

  7. 2 stars
    I followed the recipe almost perfectly. I substituted almond flour for the whole wheat as that’s what I had on hand and it was mentioned in a review. There is a lot of liquid in this recipe. The batter was so runny I had to pour it into a 4-cup measure and then pour into my cupcake papers, which I had to use because my pan isn’t a non-stick pan. I hand to bake the muffins longer before the toothpick came out clean. Even the the bottom of the papers were wet and the cupcakes were difficult to remove from the paper. That said they were done. While they tasted good, I am not sure I would make them again. If I do I might leave out the applesauce it the yogurt.

    1. Sorry, it didn’t work out for you. Almond flour is wetter than whole wheat flour and you sometimes have to add more to get the consistency right! Glad you were still able to enjoy them!

    2. While I understand the desire to tweak a recipe, this is baking – a science. I cannot understand how someone can majorly change a recipe then say it didn’t come out good as if it’s possibly the fault of the recipe or creator. Almond flour is not a true flour, it’s ground up nuts. It is not a substitute for whole wheat flour. Gluten & grain free baking is VERY tricky which you found out. Experiment with cooking, not baking, unless you are a pro. Next time look for a recipe you have the ingredients for.

  8. 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.

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