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
    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 😊

  2. 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.

    1. 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.

  3. 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?

    1. 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!

  4. 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.

  5. 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!

  6. 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.

  7. 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.

  8. 5 stars
    Very good! Mine turned out to be more of a Banana Chocolate Muffin, as I think I added too much… Oops! Still, very good. My question is why would they stick to the paper liners so much? Is it from over baking? I have used the liners before with cupcakes and they didn’t stick, but with muffins so much is left on the liner. Did I over mix the batter maybe, so it was more sticky? I have no clue… Anyway, the recipe was easy and the taste of muffins delicious! Will try again! Thanks!

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