I love a classic muffin recipe and adding more nutrition without sacrificing texture or flavor. And these healthy Chocolate Chip Muffins are a great staple recipe to make again and again for the family.

healthy chocolate chip muffins on plate

Chocolate Chip Muffins

This should not come as a shock, but my kids love chocolate chips. (I bet yours do too!) And I’ve found that a little goes a long way in terms of enticing the kids to try new foods and adding flavor to recipes.

Which is to say: That these muffins have a base that includes whole grain flour and protein-packed Greek yogurt, and also chocolate for an extra burst of deliciousness.

They’re an easy breakfast or snack option to share with the kids—plus they freeze beautifully.

ingredients in chocolate chip muffins

Ingredients You Need

To make this recipe you need:

TIP: See the Notes at the bottom of the recipe for allergy-friendly swaps.

how to make chocolate chip muffins step by step process

Step-by-Step Instructions

Here’s a look at the process involved in making this recipe. Scroll down for the full recipe at the bottom of the post.

  1. Preheat the oven and grease a standard muffin pan.
  2. In a medium bowl, stir together the dry ingredients.
  3. In another bowl, stir together the wet ingredients.
  4. Gently stir the two mixtures together. Stir in the chocolate chips.
  5. Divide batter among the prepared muffin tin.
  6. Bake until the edges are lightly golden brown and the centers are cooked through.

TIP: These are delicious served warm or at room temperature.

healthy chocolate chip muffins on wire rack

Frequently Asked Questions

What is the secret to making moist muffins?

In this recipe, it’s whole milk yogurt, which lends moisture and also protein and calcium. It produces a seriously fluffy muffin.

What’s the best way to store these?

You can store them for up to 3 days at room temperature or in the fridge for up to 5 days. (If storing in the fridge, I recommend letting them sit at room temperature for a few minutes before eating or warming for 15 seconds in the microwave as they firm up a bit when cold.)

You can also freeze them in a freezer bag, once they are fully cooled, for up to 3 months.

chocolate chip muffin in lunchbox

Best Tips for Success

  • 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.
  • 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 ¾ cup. Add ¼ cup milk and add ¼ 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.
  • You may also like Yogurt Muffins, Banana Chocolate Chip Muffins, and Pumpkin Chocolate Chip Muffins.

I’d love to hear your feedback on this recipe if you try it, so please comment below to share!

chocolate-chip-muffins-on-white-plate

Healthy Chocolate Chip Muffins

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 17 votes
Prep Time 10 minutes
Cook Time 14 minutes
Total Time 24 minutes
Cuisine American
Course Breakfast
Calories 131kcal
Servings 12

Ingredients

  • 1 1/2 cups whole-wheat flour
  • 1 teaspoon baking powder
  • ½ 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

Instructions

  • 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 ¼ 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.

Notes

  • 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 ¾ cup. Add ¼ cup milk and add ¼ 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.

Nutrition

Serving: 1muffin, Calories: 131kcal, Carbohydrates: 18g, Protein: 5g, Fat: 5g, Saturated Fat: 3g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 1g, Cholesterol: 38mg, Sodium: 147mg, Potassium: 110mg, Fiber: 2g, Sugar: 6g, Vitamin A: 160IU, Calcium: 58mg, Iron: 1mg
Tried this recipe?Rate in the comments and tag @yummytoddlerfood on IG!

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Comments

  1. 5 stars
    Made these today with a gluten free flour mix and subbed the dairy yogurt for cashew milk yogurt. Also used mini chocolate chips.

    These were an absolute hit! The texture and flavor were so perfect.

    Excellent recipe! Thank you for sharing.

  2. The metric version is WAY off. It’s telling us to use like half the amount of flour that it should be. This is the second time I’ve made super wet, inedible muffins and I’ve just realized this is why. I usually love your recipes and thought you might want to fix this!

    1. Oh my gosh, I have no idea how that happened and I’m truly sorry. I ran it again through the system I use and crossed checked it with King Arthur. Thank you for letting me know!

  3. 5 stars
    This is our favorite muffin recipe! I substitute lactose free sour cream for the yogurt and oil for the butter and they always come out fantastic. Thank you for all of your great recipes!

  4. Loved this! I was wondering what to do with choco chips and making these just made my day! So soft n fluffy! I didn’t know you can make muffins with yogurt. Also I used honey as I didn’t have maple syrup. My toddler thinks it’s not delicious just by looking at it because to him chocolate is love and that “brown” in color. So I did some nutella spread on top. Win win!

  5. Hi! Love your recipes. They are a life saver for me as a working mom. I def want to make these (I eat everything I make my kid and these look delish!) and have a quick question – at what age did you introduce chocolate chips?

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