Healthy Chocolate Chip Muffins are made with better-for-you ingredients, offering great flavor and texture. They’re moist, soft, and packed with mini chocolate chips!
Try our refined-sugar-free Healthy Banana Muffins, Banana Chocolate Chip Muffins, or Healthy Pumpkin Muffins next!
A Healthy Chocolate Chip Muffin Recipe
While healthy means something different to every individual, my philosophy with these muffins is simple — I wanted to create a really tasty bakery-style inspired muffin but with better-for-you ingredients. Because what’s the point of suffering through a muffin without a great flavor and good texture?!
These muffins are deeply flavorful with a wonderful texture– all while incorporating nutritious ingredients. This results in a breakfast, snack, or dessert that will actually be satisfying while also being more satiating (fills you up for longer)!
Ingredients
- Whole wheat flour: A great alternative to white flour.
- Egg: Adds protein, flavor, color, and richness.
- Coconut oil: Measure in the melted form for healthy chocolate chip muffins.
- Greek yogurt: My fave is Honey Vanilla Greek yogurt by Greek Gods.
- Vanilla: Optional, adds a subtle flavor.
- Baking powder, salt: Essential dry ingredients. Use baking powder, not baking soda!
- Brown sugar: Less sugar than typical muffin recipes.
- Mini chocolate chips: The key to these healthy muffins!
Quick Tip
Want to make healthy chocolate chip cupcakes? Prepare these muffins and then add a Healthy Buttercream Frosting on top!
How To Make Healthy Chocolate Chip Muffins
The full recipe card is down below; here are my top tips for making these muffins:
- Cool coconut oil: Melt the oil and let it cool to room temp to prevent clumping when mixed with cooler ingredients.
- Room-temp ingredients: Ingredients that are the same temp mix better, creating fluffier muffins.
- Grease muffin tin: Avoid muffin liners as the batter sticks; grease the muffin cups and use a good pan for easy release.
- Elevate baked muffins: Cool muffins on a rack to prevent moisture buildup and stickiness.
Storage
Chocolate Chip Muffin Storage
Store in an airtight container in the fridge; let stand at room temperature for 30 minutes to 1 hour before eating — then microwave for 5-10 seconds to warm through. They’re best enjoyed within 2-3 days.
More Baked Goods
- Strawberry Scones made with Greek yogurt and fresh strawberries
- Gluten-Free Zucchini Muffins naturally sweetened with dates
- Healthy Ice Cream without bananas! We actually use sweet potatoes!
- Applesauce Brownies with blended oats instead of flour
- Healthy Fruit Tart with Greek yogurt and fresh berries
Chocolate Chip Muffins
Equipment
Ingredients
- 1 cup white whole-wheat flour or regular all-purpose flour
- 1 tablespoon cornstarch
- 1-1/2 teaspoons baking powder
- 1/2 teaspoon salt
- 3/4 cup miniature chocolate chips
- 1 teaspoon vanilla extract
- 1 large egg at room temperature
- 1/2 cup vanilla Greek yogurt at room temperature, see note 1
- 1/2 cup light brown sugar lightly packed
- 1/4 cup coconut oil measured when melted
Instructions
- Set out the egg and Greek yogurt to come to room temperature (see note 2). Melt and then measure the coconut oil and set aside to get to room temperature—don’t add hot oil to wet ingredients (it will seize!).
- Preheat oven to 350°F. Generously grease 9 cavities on a regular-sized, 12-cavity muffin pan and dust the cavities generously with flour. Don’t use paper liners (these muffins stick; see note 3). Set aside.
- Add flour, cornstarch, baking powder, salt, and mini chocolate chips to a bowl. Mix to combine.
- In another bowl, add the vanilla extract, room-temperature egg, room-temperature Greek yogurt, brown sugar, and room-temperature coconut oil. Briskly whisk ingredients together until smooth.
- Add the dry ingredients to the wet ingredients and stir until *just* combined. Overmixing will result in dense muffins.
- Divide the batter evenly into the 9 prepared cavities of the muffin pan. If desired, sprinkle 1/2 teaspoon brown sugar on the tops of the muffins (optional but great crunch). Fill the remaining cavities halfway with water (to ensure even baking). Bake for 18–22 minutes or until lightly browned at the edges and a toothpick when inserted into the center comes out clean or with moist crumbs; be very careful to not overbake these muffins or they won’t be nearly as soft and moist.
- Remove from oven and allow to cool in the pan for about 5 minutes before removing the muffins onto a cooling rack to finish cooling. Do not cool muffins in the pan. The muffins need to be elevated so air can circulate around all sides as they cool. Otherwise, moisture (from the heat of the muffins) will condense on the bottoms, making them damp and slightly sticky.
Video
Recipe Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Tried these this morning with my kids and they were SO tasty! We followed all of the directions except the sifting part, lol.
I will be making a second batch today and will add pecans 🙂
Thank you for this amazing recipe!
I’m so glad you guys enjoyed this! Pecans sounds delicious with these! Thanks! 🙂
Okay, these we’re AMAZING, a huge hit with my boyfriend. I subbed 1/4 of the flour for 1/4 cup of golden flaxseed, and you can’t even tell it’s there when you eat it, still super moist and decadent.
Yay! Love hearing that! Thanks so much for the comment 🙂
These look delish! Making them this weekend
Hope you love them! 🙂
How many calories and fat in this recipe?
I used your recipe today and to honest I didn’t expect it gonna be that Delicious !
I don”t have vanilla flavored Greek yogurt so I used honey flavored yogurt without added sugar instead I think it works
also I used 100% choco bar ..
thanks for that incredible recipe .. your family is lucky to have you ^_^
Have a nice day .
You are so kind; thank you for your comment! I’m so glad you enjoyed these muffins ?
Dear, I really enjoy and appreciate your work ! Thank you so much !
AMAZING!! Love anything that involves chocolate and healthy in the same sentence.
These muffins look incredible! We are muffin-a-holics over here and big fans of Greek yogurt in about everything:-)!
hey girl- love the post! Kids will be kids! ha And these muffins look so yummy! Y’all have a great weekend!