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

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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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!

  9. 5 stars
    I’ve been looking for low sugar recipes that actually have lower amounts of sugar instead of simply replacing higher amounts of sugar with something else (like maple syrup or coconut sugar) that is still sugar. They’re hard to find, especially with chocolate! This recipe was great. The texture and crumb is perfect and it is satisfying chocolatey without being bitter. I pureed the sugar with mint leaves for some additional flavor. Thanks for sharing!

  10. 4 stars
    I used All Purpose Flour since I don’t have Whole wheat flour and used dark chocolate chips. It turned out moist and the kids loved it. Thanks for the recipe

  11. 5 stars
    Used non fat greek yogurt and 1% milk; used a 50/50 mix of canola and olive oil and added 1/4 tsp of baking powder to counter the heavier olive oil and give more lift. Came out great but needed 5 min mire baking.

  12. Delicious. Made these for the grandkids who were over the moon with these healthy muffins. Perhaps they put more than 2/3 of a cup in the muffin tins as they all had walrus noses?! Still a big hit. Thanks for the recipe.

  13. 5 stars
    So moist, so chocolaty! I added some white chocolate chips too, and only had vanilla Greek Yogurt so reduced the sugar to 1/3 cup. Raving reviews from the kiddos too :-). These are really more like a cup cake, and may even use them for birthdays in the future.

  14. 5 stars
    Lovely recipe! I halfed it and made 6 wonderful muffins with some substitutions. Used only whole wheat pastry flour, sour cream instead of greek yogurt, coconut sugar instead of granulated and dark choc chips instead of semi-sweet. Baked for 13 minutes. Muffins came out moist and delicious!

  15. 5 stars
    Thanks so much for sharing this wonderful recipe. I am on a very restricted diet due to health reasons and found your recipe. I made the following changes but they still turned out delicious. rice flour instead of whole wheat flour, almond meal instead of all purpose flour, coconut sugar instead of granulated sugar, 1/4 cup cacao instead of cocoa powder, no cinnamon, raspberries instead of choc chips, 2 x tablespoons of ground flaxseed and 6 x tablespoons of water instead of 2 x eggs, natural coconut yogurt instead of Greek yogurt, coconut oil instead of other oils, 1/2 a vanilla bean (scraped) instead of vanilla extract. My recipe made 9 delicious moist muffins which we took on our picnic and bike ride today. I found they required 25 minutes baking time.

  16. 5 stars
    Thank you Lauren for such a fantastic recipe! Will try adding chocolate whey protein powder next time. These are less oily than Costco muffins; these are still an occasional treat. Will try your other recipes as they look delicious! Thank you!

  17. 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!

  18. 5 stars
    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 🙂

  19. 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.

  20. 5 stars
    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.)

  21. 5 stars
    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

  22. 5 stars
    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

  23. 5 stars
    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!

    1. 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!!

  24. 5 stars
    Made these for breakfast and they really hit the spot. Delicious and moist. Am not a chocoholic by any stretch but when i do crave it I Really want something with good chocolate flavor, this hit the mark. Was just wondering if your nutrition info is for the full fat yogurt and milk and for using canola oil.

    1. Hi Mary, thank so much for sharing! The nutritional facts are using low fat Greek yogurt and coconut milk.

  25. I made these today and so happy to have found a healthy double chocolate muffin recipe! They are perfect!

  26. I made these for an after school treat today. They were fabulous! Perfectly sweet (not too sweet!) and chocolatey! My kids devoured them. Next time I’ll have to double it! Thanks for the recipe!

  27. Made these muffins this morning for my 3 teens as a Sunday morning treat. We all loved them. Substituted coconut oil for canola. Thanks for sharing this recipe! 🙂
    Delicious!

  28. Just made these a few minutes ago. OMG, they are awesome!!! I was craving something sweet and chocolatey, but not a cupcake or a 2000 calorie muffin. These are perfect and hit the spot. Thank you so much for this recipe!!!!!

    1. I’m so glad you liked them! They are the perfect lower-calorie muffin to satisfy a sweet tooth 🙂

    1. Hi Krystal, plain yogurt would taste bet but the vanilla will work too. I would leave out the vanilla extract.Good luck, hope you like them! 🙂

  29. These chocolate muffins look seriously so rich and delicious!! I love using yoghurt in baking as it always makes everything so much more moist and gives a slight tangy taste so I bet these taste amazing.

  30. OH yum I love muffins – and greek yogurt is such a great way to add moisture and protein!! Love love love

  31. Is there anything better than chocolate for breakfast? I think not! 😉

  32. I just started a new “diet”so I’ve been craving chocolate. I think I could still have these and stick to my plan.

    1. I hope you do and let me know how you like them! Any ways you can find to sneak chocolate into a diet are the best!

  33. I actually made these just after you posted this on the blogger life! just bit into my first one and they’re delicious, thanks!

  34. I almost didn’t click on here as I am holiday dieting but they looked too good to pass up!! Have printed off for my recipe folder and will let you know how I get on 🙂

        1. Applesauce would be a good substitute. The calorie difference in wheat vs white flour is not very different.