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Healthy Chocolate Chip Muffins

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These healthy chocolate chip muffins are so good you won’t realize they aren’t packed with sugar! Shredded zucchini makes these muffins moist and delicious with just the right amount of sweetness.

healthy chocolate chip muffins on piece of wood
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The word healthy is very relative and it depends on what someone’s eating regimens and goals are as to whether they feel a food is healthy. When I am able to adapt a recipe to include less sugar and more whole type foods I feel I have made it healthier for my family’s needs.

One easy substitution is to use whole wheat flour in baked goods. The whole wheat flour is a better source of fiber and other nutrients then bleached white flour.

Another way to make a healthier muffin is to reduce the oil in the recipe. Most muffins and baked goods call for quite a bit of oil. This adds so many calories!

It amazes me that I can swap out the oil for ingredients like applesauce and nonfat Greek yogurt and get great results.

The last way to make muffins healthier is to reduce the sugar content. In this recipe, I have done that by replacing some of the sugar with applesauce. I have also reduced the number of chocolate chips I use! The taste is still super and the calories are much friendlier to my waistline!

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This recipe calls for many basic muffin ingredients with a few hidden surprises! The end result will delight you I know! My kids love how these always turned out perfectly!

close up image of healthy chocolate chip muffins on a piece of wood


Some people call these zucchini muffins, but I will be honest. My kids eat them better when I call them healthy chocolate chip muffins, LOL. It is all in the delivery, right? 🙂

Muffins are a standby at our house, like my Air Fryer Chocolate Chip Muffins. We eat them for breakfast, desserts, in school lunches and as after school snacks. They are also great to take in a basket to someone in the neighborhood.


Start off by preheating the oven to 350 degrees F.

Grab your regular sized muffin pan and grease the muffin cups with nonstick cooking spray or add muffin liners to the pan. I personally love my silicone muffin cup liners!


In a large bowl combine the unsweetened applesauce, brown sugar, egg, plain nonfat Greek yogurt, and vanilla extract. Whisk these ingredients together until they are well combined.

applesauce, brown sugar, egg, plain nonfat Greek yogurt, and vanilla extract in a white mixing bowl with a whisk in it


Now add the following ingredients to your bowl of batter: whole wheat flour, baking powder, baking soda, salt and cinnamon. Stir these dry ingredients into the wet ingredients until they are combined.

adding dry ingredients to mixing bowl for healthy chocolate chip muffins


If you haven’t already peeled and shredded your medium zucchini you can do that now.

Add the shredded zucchini to the bowl and stir to combine.

adding shredded zucchini to healthy chocolate chip muffin batter


Now spoon the muffin batter into the muffin cups until they are about 2/3 of the way full.

healthy chocolate chip muffins batter in muffin cups in a muffin tin


It is time to add the chocolate chips. You will put 3 chocolate chips on top of the batter in each muffin cup. You will be surprised that it only takes 3 chocolate chips to add that flavor!

adding chocolate chips to the batter in muffin tin for healthy chocolate chip muffins


Place the muffin pan in the oven and bake for 30 minutes or until they are completely cooked in the center. You can check for doneness by inserting a toothpick into the center of the muffin and see if it comes out clean.

When the muffins are done baking remove the pan from the oven and leave the muffins to cool in the pan for about 10 minutes. Remove the muffins from the pan after 10 minutes and place them on a wire rack to finish cooling completely.

healthy chocolate chip muffins on large wooden spatula

I am sure you will want to print this recipe to keep in your kitchen binder! It is an easy go-to muffin recipe we use all the time. You can print off the complete ingredients and instructions via the recipe card below.

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📋 Recipe

healthy chocolate chip muffins on large wooden spatula

Healthy Chocolate Chip Muffins

Corinne Schmitt
These healthy chocolate chip muffins are packed with nutritious ingredients like shredded zucchini and unsweetened applesauce. They are moist and flavorful for breakfast or a snack.
5 from 4 votes
Prep Time 15 minutes
Cook Time 30 minutes
Total Time 45 minutes
Course Dessert
Cuisine American
Servings 12 people
Calories 105 kcal


  • 1/3 cup unsweetened applesauce
  • 1/3 cup brown sugar
  • 1 egg
  • ½ cup plain nonfat Greek yogurt
  • 1 ½ teaspoons vanilla extract
  • 1 ½ cups whole wheat flour
  • ½ teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • 1 teaspoon cinnamon
  • 1 medium zucchini shredded
  • 2 tablespoons chocolate chips


  • Preheat the oven to 350 degrees. Prepare a muffin pan by greasing the cups with nonstick cooking spray or lining each cup with paper liners.
  • Combine the unsweetened applesauce, brown sugar, egg, Greek yogurt and vanilla extract in a large bowl. Whisk to mix.
  • Add the flour, baking powder, baking soda, salt, and cinnamon. Stir until just combined.
  • Add the zucchini and stir to mix.
  • Spoon the batter into the muffin tin, filling each cup 2/3 of the way full. Top each muffin with three chocolate chips.
  • Bake for 30 minutes or until a toothpick comes out clean when inserted into the center of the muffin. Allow to cool in pan for 10 minutes, then remove muffins to a wire cooling rack to cool completely.


If you are following the WW program this recipe is 3 Freestyle SmartPoints per muffin.


Calories: 105kcalCarbohydrates: 20gProtein: 4gFat: 1gSaturated Fat: 1gCholesterol: 15mgSodium: 108mgPotassium: 146mgFiber: 2gSugar: 9gVitamin A: 58IUVitamin C: 3mgCalcium: 37mgIron: 1mg
Tried this recipe?Let us know how it was!

If you loved this healthy chocolate chip muffin recipe be sure to check out these other great healthy recipes:

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a collage of healthy chocolate chip muffins with title text reading Healthy Chocolate Chip Muffins

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