These healthy Chocolate Chip Muffins have all the yummy flavor and tender texture of a classic muffin with more nutrition. They are higher in protein, lower in sugar, and so easy to make!
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 healthy Chocolate Chip Muffins have a base that includes whole grain flour and protein-packed Greek yogurt, and also chocolate for an extra burst of deliciousness.
These healthy muffins for kids are an easy breakfast or snack option to share with the kids—plus they freeze beautifully.
Why This Recipe Works
A super simple one-bowl method pairs with nutritious, yet accessible ingredients to create fluffy muffins the kids will love.
(You may also like my Mini Chocolate Chip Muffins, Yogurt Muffins, and Healthy Chocolate Muffins.)
Table of Contents
Ingredients You Need
To make this Healthy Chocolate Chip Muffin recipe you need to have the following ingredients on hand and ready to go.
- Whole-wheat flour: I use whole-wheat flour in this recipe to start with a base of whole grains.
- Baking powder and baking soda: Using a combination of these rising agents ensures the muffins rise and bake through as intended. Be sure your baking soda is fresh.
- Whole milk plain Greek yogurt: This type of yogurt is thick and creamy, and adds both protein and tenderness to the muffins. You can use reduced-fat yogurt if that’s what you have on hand, but whole milk yogurt is preferred.
- Maple syrup: I sweeten this recipe with maple syrup, though you can also use honey for kids over age 1 if you prefer.
- Unsalted butter: I like to bake with unsalted butter so I can control the salt in the recipe. You’ll want to melt it and let it cool slightly before adding it to the rest of the batter.
- Eggs: I bake with large eggs, so plan to use them here so the volume of wet ingredients is correct.
- Vanilla extract: You can use pure or artificial vanilla extract in this recipe.
- Chocolate chips: You can use semi-sweet or dark chocolate chips, regular size or mini.
TIP: See the Notes at the bottom of the recipe for allergy-friendly swaps.
Featured Review⭐️⭐️⭐️⭐️⭐️
“Just made these and they are perfect—fluffy and delicious! I will definitely be making these again! Thanks for sharing!” —Emily
Step-by-Step Instructions
Here’s a look at the process involved in making this healthy Chocolate Chip Muffin recipe. Scroll down for the full recipe at the bottom of the post, including the amounts and timing.
Step 1. In a medium bowl, stir together the dry ingredients.
Step 2. In another bowl, stir together the wet ingredients.
Step 3: Gently stir the two mixtures together. Stir in the chocolate chips.
Step 4. Divide the batter into a prepared muffin tin and bake.
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Frequently Asked Questions
In this recipe, it’s whole milk yogurt, which lends moisture and also protein and calcium. It produces a seriously fluffy muffin.
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.)
Stir the batter gently. Set the timer for the lower end of the baking time range to ensure they are not ove-baked. Remove from the pan and cool on a wire rack.
How to Store
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.
Best Tips for Success
- 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.
Related Recipes
I’d love to hear your feedback on this recipe if you try it, so please comment below to share!
Healthy Chocolate Chip Muffins
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.
Equipment
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.
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!
Delicious, easy, and super for daycare lunchboxes!
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!
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!!
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 :))
These were amazing – my new favorite 🤩
Loved these!! Made them with bluebs but I think even plain would be a hit. Surely going in the rotation. Love all your recipes!
Love them and this website
I just made these for my kids and they are delicious. Definitely adding these to our rotation! Thanks for another great recipe.
Could we use almond flour for this recipe?
No, it’s not a good substitute on its own for wheat-based flours.
Delicious and easy!
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!
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.
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 ❤️❤️
You’re so welcome!
How long do we bake if making mini muffins?
It should be in the 10-12 minute range!