These super moist Whole Wheat Dark Chocolate Chip Muffins are made up of 100% stone ground whole wheat and chunks of dark chocolate for a healthier way to treat yourself.

Mixing bowl with whole wheat flour and coconut palm sugar in it with pinch bowls off to the side.

Whole wheat. And chocolate. Does that seem conflicting? I’m all about balance, so I’m totally okay with it. Especially since these are dark chocolate chips. Dark chocolate has its health benefits! It’s even believed to be protective against heart disease. So in my mind, throwing some of this bittersweet goodness into a blend with stone ground whole wheat is totally innocent ;)

I’ve been pairing my morning cup of coffee with one of these muffins every morning this week. And some nights, I’ve had them as an evening snack. I can’t help myself. A quick zap in the microwave and you get a warm fresh-from-the-oven feel complete with melty gooey chocolate and it. is. heaven.

Working with whole wheat flour can be tricky, however. You need to be sure to bring some extra moisture to that mixing bowl before you go throwing your treats into the oven. But I’m here with tips, because whole wheat flour is damn good and I want everyone to be able to enjoy it as much as I do.

Adding extra moisture to whole wheat muffins.

Grated apple and grater on a cutting board.

Whole wheat flour results in a drier texture, so adding extra moisture is imperative. This recipe contains a few ingredients that you want to be sure not to skip out on, nor make substitutions.

  • an extra egg
  • olive oil
  • unsweetened applesauce
  • one apple, peeled and grated

Are these muffins healthy?

Collage of ingredients mixed up in a mixing bowl.

Muffin cups placed in a silicone muffin tray. Half of the muffin cups are filled with cupcake batter.

Cooling rack full of whole wheat chocolate chip muffins.

Let’s be clear—no muffins are healthy. But because of the ingredients used in this recipe, these muffins can definitely be considered a smarter option that treats you while nourishing you at least a little.

  • The stone ground milling process is done without heat. Therefore, stone ground whole wheat retains all of its nutrients with the bran and germ still intact, providing all of the health benefits you want—like a healthy dose of fiber, vitamins, and minerals.
  • Dark chocolate contains some sugar, but the amounts are small; the darker the chocolate, the less sugar it contains. Ideally, you want to find dark chocolate with a cocoa content of 70% or greater. If you can’t find this in chocolate chips, no sweat. Get yourself a dark chocolate bar and roughly chop it up into chunks.
  • Unrefined sugars and sweeteners provide at least a bit of nutrition—as opposed to processed sugars—since they still hold natural minerals and nutrients like phosphorus, calcium, iron, magnesium, and potassium. Refined sugars are stripped of these things. So although unrefined sugars shouldn’t be considered good for you, they’re a much better alternative. Unrefined sugars and sweeteners include, to name a few, maple syrup, honey, agave nectar, unsulphered molasses, coconut sugar, sucanat, fruits, and date sugar.
  • This recipe contains olive oil instead of butter, but it’s important to remember that they’re both 100% fat. Olive oil, however, has way less saturated fat and no dietary cholesterol.

Side shot of muffins on cooling rack.

Other muffin recipes I love.

If you make this recipe, be sure to tag me on Instagram @killing__thyme!

Whole wheat chocolate chip muffins lined up on a cooling rack.

Get the Recipe:

Whole Wheat Dark Chocolate Chip Muffins

These super moist Whole Wheat Dark Chocolate Chip Muffins are made up of 100% stone ground whole wheat and chunks of dark chocolate for a healthier way to treat yourself.


  • 2 cups 100% stone ground whole wheat flour
  • 1 cup unrefined sugar, I used coconut palm sugar
  • 2 tsp baking soda
  • 1 TBSP ground cinnamon
  • 1/2 tsp kosher salt
  • 2 large eggs
  • 1/2 cup extra virgin olive oil
  • 1/2 cup unsweetened apple sauce
  • 2 tsp vanilla extract
  • 1 large apple, peeled and grated (about 1.5 cups worth of grated apple)
  • 1 cup dark chocolate chips
  • 1/2 cup toasted shredded coconut, You can omit this entirely, or substitute with chopped nuts or dried fruit, like cranberries.


  • Muffin tray
  • Muffin cups


  • Preheat oven to 350º F. Line a muffin tray with paper muffin cups.
  • In a large bowl, whisk together the flour, sugar, baking soda, cinnamon, and salt; set aside.
  • In another bowl, whisk together the eggs, olive oil, applesauce, and vanilla extract. Once cohesive, gently stir in the grated apple, chocolate chips, and toasted coconut if using. (Or your substitution.)
  • Slowly add the dry ingredients to the wet ingredients, stirring constantly, until everything is well combined.
  • Spoon the mixture into the paper cups right up to the tops of the cups.
  • Bake for 20-25 minutes, or until a cake tester/toothpick comes out clean when tested.