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—including healthy muffins for kids—and adding flavor to kid-friendly recipes.
Quick Look: Healthy Chocolate Chip Muffins
- Prep Time: 10 minutes
- Cook Time: 14 minutes
- Total Time: 24 minutes
- Serving: 12
- Flavor Profile: Moist chocolate chip muffins with vanilla undertones
- Difficulty: Easy, perfect for snacks and breakfasts
- Why to Make: It’s a one-bowl muffin that’s yummy and nutritious
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Table of Contents
These healthy Chocolate Chip Muffins have a base that includes whole grain flour for a protein-packed Greek yogurt muffin that tastes so good.
These toddler muffins are an easy breakfast, snack, or toddler lunch idea 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 Chocolate Chip Muffins the kids will love.
(You may also like my Mini Chocolate Chip Muffins, Yogurt Muffins, and Healthy Chocolate Muffins.)
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
How to Make Healthy Chocolate Chip Muffins
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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Healthy Chocolate Chip Muffins FAQs
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.
- Pair with a Cherry Smoothie, Fruit Cup, or Vanilla Yogurt.
More Easy Baked Goods
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.
i made these muffins for my 3 year toddler and she loved them they turned out to be really good
The batter turned out too dry for us. What would you suggest adding in this case?
You could reduce the flour to 1 1/4 cups
My 3 year old granddaughter and I made these, they are delicious! The muffins are pretty simple to make and use common ingredients. They have a hearty flavor due to the whole wheat flour.
What would the baking time be for mini muffins?
Usually mini muffins are 10-12 minutes.
Made these muffins today- my toddler loved them. Total win in my book!
Hi! These look great but I don’t have Greek yogurt only regular plain yogurt. Think that could work or would it be too wet? Could I compensate by adding a little more flour? Thanks!
Hi- it should work fine, you could add 2 tbsp more flour if you’d like. Enjoy!
Do you think strawberry yogurt would work?
I haven’t tried it so I’m not sure how the flavor would be but it should from a baking standpoint.
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.
When substituting in berries for the chocolate chips, would you use fresh or frozen? Thanks!
You could do either!
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!
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!
what could be the substitute of maple syrup?
You can use honey or use the same amount of sugar plus 2 tablespoons milk
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!
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!
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?
We did them around 18 months ish.
Another winner! These are delicious!!!
I’m so glad to hear it!