Web Analytics

Home > Desserts > Muffins > Healthy Chocolate Chip Muffins

Healthy Chocolate Chip Muffins

You know those big bakery-style chocolate muffins that are so soft inside and rich in chocolate? Follow our recipe and make at home these delicious treats everyone loves. 

Semi-sweet or bittersweet chocolate is best! They give you the perfect balance of sweet and rich, deep chocolate flavor. Milk chocolate is more sugar than actual cocoa solids which just won’t serve this recipe well.

So what makes these chocolate chip muffins healthy? A couple of things! First off, we use whole grain spelt flour in this recipe. Then we add proten packed Greek yogurt, instant oat flakes and coconut oil. And finally, we sweeten these delicious muffins with honey and just a small amount of dark muscovado sugar. So these muffins are made with a choice of healthy ingredients you can feel good about.

Earlier I mentioned there is NO butter in this recipe. Let’s talk more about that! Since I cut the butter out, I needed to replace it with another ingredient that would add both moisture and flavor. I also wanted to keep these muffins on the healthier side. I tested the recipe with olive oil, coconut oil, and a combination of both, and am happy to say all three variations are winners! If you choose to use olive oil, I do recommend using a brand that isn’t intensely flavored. A milder olive oil will work best. Also, the taste of oil in the finished product isn’t strong, so don’t worry about your muffins being overly flavored by either one.

how to make healthy chocolate chip muffins

For making these muffins you'll need a muffin tray, 2 mixing bowls and spatula. No hand mixer or fancy appliances required!

Combine in a large bowl flour, sugar, baking powder, baking soda, salt, instant oat flakes and set aside. In another bowl, whisk using hand whisk egg, yogurt, honey. Now, gently pour the wet ingredients into the flour mixture and using a spatula fold until combined. Fold in the oil and stir couple of times again. Divide the batter among muffin cases, place tray in the oven and bake for about 15 minutes. Cool muffins in the tray for 5 minutes, then transfer them to a cooling rack.

storing healthy chocolate chip muffins

Store the muffins at room temperature in an airtight container. Also, a great trick is to freeze the raw batter in the cupcake lines then you can defrost and bake-off fresh chocolate muffins whenever you want them.

Something like a chocolate chip muffin is best enjoyed within the first 48 hours to have it at its very best. Personally, I ate mine in the first 48 minutes.

They also freeze quite well, so you can also pop half the batch in the freezer if you want to save some for another day. I always find muffins taste best on day one – especially fresh out of the oven – but these will stay fresh for up to 3 days if you store them in an airtight container.

This recipe makes exactly 12 muffins… and they go FAST! So if you’re serving a crowd, consider making 2 dozen Even picky kids love this healthy banana muffins recipe!

  • Use bittersweet or semi-sweet chocolate for this recipe so you get an extra rich chocolate muffin
  • Freeze the raw batter in the cupcake liners to be baked off fresh anytime
  • Just like a pancake batter, just mix until the muffins come together because you don’t want to over mix
  • Be careful not to open the oven door during the first 20 minutes of baking or the chocolate muffins can deflate
  • Eat your muffins within 48 hours to have them at their best

more delicious muffins to try:

Healthy Chocolate Chip Muffins


  • 280g whole grain spelt flour
  • 60g instant rolled oats
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/4 teaspoon salt
  • 50ml coconut oil or mild olive oil
  • 40g muscovado sugar
  • 2 tablespoons honey
  • 2 medium eggs, at room temperature
  • 160g Greek yogurt, at room temperature
  • 1 teaspoon vanilla extract
  • 200g dark chocolate chunks (60 - 70% cocoa)


  1. Preheat the oven to 220°C (430°F). Line 12-hole muffin tray with standard paper cases.

  2. In a large bowl combine flour, cocoa powder, baking powder, baking soda and salt.

  3. In another bowl, whisk the eggs, sugar, melted butter, yogurt and vanilla extract until the sugar is completely dissolved.
  4. Pour wet ingredients into dry and fold together using a silicon spatula until everything is combined and you get a homogenous texture. Stir in chocolate chunks and mix everything. Don't overmix so your muffins don't get dense and tough. The dough should be very thick.

  5. Spoon the batter into prepared muffin cases filling all the way to the top. Once you fill the muffin cases, top with remaining chocolate chips and leave them to rest for 10 minutes. This allows the flour in the batter to fully hydrate.

  6. Bake the muffins at 220°C (430°F) for 5 minutes, then reduce the oven temperature to 180°C (360°F) and continue to bake for another 8 - 10 minutes or until the tops are lightly golden brown. Check if the muffins are ready by inserting a skewer into the centre. It should come out clean. Leave the muffins to cool in the muffin tray for 2 - 3 minutes then transfer them to a serving plate.