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.
I love this recipe. 100% whole wheat flour is awesome. I used some sour cream/yogurt combo, what I had on hand. I also replace butter with avocado oil; just easier for me. We added shredded coconut as well…..delicious.
I just made these today and the whole family loves them! The only thing is, they came out a little dry -I did replace the maple syrup with honey – could that be why? Would adding a splash of milk help?
What is the cooking temp and time if I were to use a mini muffin tin?
Still bake at 375 degrees F. I would decrease the time to 10-12 minutes, making to check frequently and removing when the edges are lightly golden brown and a cake tester inserted into the center comes out cleanly.
Temp is the same, minis usually are 12-14 minutes.
These are really good! I agree with other reviewers that the texture is really great compared to other “healthy” muffin recipes I’ve tried!
I only had nonfat greek yogurt on hand so I used that and added a few tablespoons of brown sugar and 1 extra tablespoon of butter to make up for it, seemed to work perfectly! I also subbed Lily’s chocolate chips for half of the chocolate chips.
***Note- the calories listed seem way off. I know I modified a few things, but my calorie count comes to 235 calories per muffin. (I did add calories from butter and sugar, but I subtracted with the non fat yogurt)
So I’m not sure how the original could be only 131? Just a warning to those trying to be in a calorie deficit like me
Hello! I only have a regular muffin tin — do you have a suggestion for temp or timing? Thanks!
Same temp, about 14-16 minutes for time.
Can you use all purpose flour instead of whole wheat?
I haven’t made them that way but it might work. They may need an extra 2 minutes or so in the oven.
Love this recipe!
We use kite hill unsweetened vanilla Greek yogurt and bobs red mill egg replacer for the recipe due to allergies and it works great. The only thing I do is add almond milk to make the batter thinner and easier to scoop!
I made these 3 weeks in a row now!
Hi, making these for kindergarten…. could I add some cocoa powder to the mixture, just to give the muffins a brown, chocolaty look? If so, would 2 tablespoons be enough? Would I reduce the amount of flour by the same amount? Thx!
That should work! I would then reduce the flour by the same amount.
Just made these and they are perfect! Sometimes the density of yogurt foods can be odd, but these are fluffy and delicious! I will definitely be making these again! Thanks for sharing!
I am so glad you enjoyed them!
Hello! We loved the recipe. But I have a question, why does it say 1g Trans fat?
There is sometimes a trace amount in chocolate that registers as 1 gram of trans fat.
WOW!! I never comment on recipes. This one blew my mind! We use Einkorn wheat due to sensitivities and the texture of it is always slightly different due to the flour. This recipe gave us the texture of a “regular” muffins that we’ve missed so much! Hands down our only muffin base from now on! THANK YOU!
I’m so glad to hear this and thank you for commenting!
Just made these for easy school morning breakfasts for my toddler and two teen daughters. They are delicious!
WOW! Literally taste like cookie dough. I used Two Good vanilla yogurt and 1 cup of regular flour 1/2 cup of oat flour and Lily’s sugar free chocolate chips. AMAZING!
My 4-year-old is obsessed with these. Asks for them every morning 🙂 Great recipe, very tasty and I feel good about her eating these. Especially as often as she does, haha.