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Healthy Chocolate Chip Muffins

Amy Palanjian
Loaded with whole grains and protein, these healthy Chocolate Chip Muffins are a really great standard recipe to turn to whenever you're in the mood!
5 from 12 votes
Prep Time 10 mins
Cook Time 14 mins
Total Time 24 mins
Course Breakfast
Cuisine American
Servings 12
Calories 131 kcal


  • 1 1/2 cups whole-wheat flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1 cup whole milk plain Greek yogurt
  • 1/3 cup maple syrup
  • 1/4 cup unsalted butter (melted and slightly cooled)
  • 2 eggs (lightly beaten)
  • 2 teaspoons pure vanilla extract
  • 1 cup chocolate chips


  • Preheat the oven to 375 degrees F. Grease a 12-cup standard muffin pan with nonstick spray.
  • In a medium bowl, stir together the flours, baking powder, baking soda, and salt.
  • In another bowl, stir together the yogurt, maple syrup, eggs, butter, and vanilla.
  • Gently stir the yogurt mixture into the flour mixture.
  • Stir in the chocolate chips.
  • Divide batter among the prepared muffin tin, using about 1/4 cup batter in each cup.
  • Bake for 14-16 minutes, or until the edges are lightly golden brown and a cake tester inserted into the center comes out cleanly. Remove from oven, then transfer muffins to a wire rack to cool fully.


  • Once cooled, store in an airtight container for up to 3 days at room temperature. Store in the fridge in an airtight container for up to 5 days. Warm slightly to serve from the fridge. You can also freeze the muffins in a freezer bag with as much air removed as possible for up to 3 months. Thaw at room temperature or in 15 second increments in the microwave.
  • I like using whole milk Greek yogurt in this recipe. You can use regular style yogurt if you prefer.
  • Dairy-free: Use a nondairy Greek style yogurt like the plant-based options from Siggis and a neutral oil like canola in place of the butter.
  • Egg-free: Reduce the yogurt to 3/4 cup. Add 1/4 cup milk and add 1/4 teaspoon additional baking soda.
  • Gluten-free: Use cup for cup gluten-free all purpose flour.
  • Dice up as needed for younger eaters.
  • Top with butter, nut butter, or jam as desired.
  • Try half chocolate chip and half blueberries, diced strawberries, or diced cherries as a yummy alternative.


Serving: 1muffinCalories: 131kcalCarbohydrates: 18gProtein: 5gFat: 5gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 1gCholesterol: 38mgSodium: 147mgPotassium: 110mgFiber: 2gSugar: 6gVitamin A: 160IUCalcium: 58mgIron: 1mg
Keyword chocolate chip muffins, healthy chocolate chip muffins
Did you make this recipe?Rate in the comments and tag @yummytoddlerfood on IG!