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two chocolate muffins on plate

Healthy Muffin Recipes: Healthy Chocolate Muffins

  • Author: Alexis Joseph
  • Prep Time: 10 minutes
  • Cook Time: 16 minutes
  • Total Time: 26 minutes
  • Yield: 10 muffins 1x
  • Category: Desserts
  • Method: Oven
  • Cuisine: American
  • Diet: Vegetarian


The best tall and fluffy Healthy Chocolate Muffins made with whole grains and naturally sweetened! Moist and not overly sweet to conquer chocolate cravings, plus 5g of protein per muffin. These taste like classic chocolate cupcakes!


Units Scale
  • 1 cup whole wheat flour*
  • 1/2 cup almond flour
  • 1/3 cup unsweetened cocoa powder (or cacao powder)
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1/2 tsp fine sea salt
  • 1/2 cup milk of choice (oat, cow's, almond, etc)
  • 1/2 cup pure maple syrup
  • 2 large eggs
  • 1/4 cup avocado oil (or melted and cooled coconut oil)
  • 1 1/2 tsp vanilla extract
  • 1/2 cup chocolate chips, plus more for topping


  1. Preheat the oven to 425 degrees Fahrenheit and grease a muffin tin with cooking spray.
  2. In a large mixing bowl, stir together whole wheat flour, almond flour, cocoa powder, baking soda, baking powder, and salt.
  3. In a medium bowl or liquid measuring cup, whisk together milk, maple syrup, oil, eggs, and vanilla.
  4. Pour the wet ingredients into the dry ingredients, stirring with a wooden spoon just until combined. Gently fold in ½ cup chocolate chips.
  5. Spoon batter evenly into 10 muffin cups. Top with additional chocolate chips if you like! Bake for 8 minutes at 425°F and then reduce the heat to 350°F (keeping muffins in oven) and bake for another 9-10 minutes, or until a toothpick comes out clean. Cool muffins in tin for 10 minutes before transferring to a wire rack to cool.


*All purpose flour, white whole wheat flour, or whole wheat pastry flour can be substituted for the whole wheat pastry flour. There are no substitutions for the almond flour as it contributes necessary fat for the recipe!

For sweeter muffins, you can increase maple syrup to ¾ cup.

Keywords: healthy chocolate muffins