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!

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

Ingredients

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
    Easy and delicious!!!! I make my toddler a lot of your muffin recipes. I don’t eat bananas so I never get to try most of them, but this muffin I got to try- yum! I made them mini size and they turned out wonderful. Thank you for all of your recipes!

  2. 5 stars
    These are delicious! My chocolate-loving 3 year old and I both loved them. I subbed peanut butter for the butter to add a little more flavor and protein. The batter seemed a bit thick because pb is thicker than melted butter, so I added 2 Tbsp of milk. Will definitely make again!

  3. 5 stars
    These muffins are so delicious and fluffy and very very quick and easy! I love every single one of your recipes that we’ve tried. Thank you!!

  4. 5 stars
    Thanks so much Amy! Your blog became my go-to for feeding my toddler AND my husband, who’s sometimes even more difficult to please :))

  5. 5 stars
    Loved these!! Made them with bluebs but I think even plain would be a hit. Surely going in the rotation. Love all your recipes!

  6. 5 stars
    I just made these for my kids and they are delicious. Definitely adding these to our rotation! Thanks for another great recipe.

  7. 5 stars
    I made these with my 2.5 yo and they were great! Great texture and plenty sweet for us. We’ll be making them again soon!

  8. 5 stars
    I made these with my 2.5 yo and they turned out so well! Great texture and plenty sweet for us. We’ll be making these again soon.

  9. Thank you so much for providing the egg free dairy free and gluten free options… from a tired mama trying to feed her little ones w food sensitivities ❤️❤️