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 mins
Cook 15 mins
Total 25 mins
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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
    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!

  2. 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!

  3. 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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