Double Chocolate Mini Muffins

Guilt free Double Chocolate Mini Muffins pack a guilt-free punch into every bite. These chocolatey treats are made with oatmeal and whole wheat flour instead of white flour and use Greek yogurt and applesauce in place of oil. The simple substitutions help to reduce the calories and fat while boosting the protein, whole grains, and fiber in each bite.

Bite-sized Double #Chocolate Mini Muffins guilt-free lunchbox treats via @holleygrainger Click To Tweet

The muffins are the ideal size for a child’s lunchbox or after school snack but are certainly grown-up friendly too! In the picture above, you can see that I included them in Frances’s and Ellie’s school lunchbox. (See Healthy School Lunchbox Meal Plans: Week 3) I personally love to eat them for breakfast with a smear of peanut butter on top–MMM! And Frances loves to eat as many as she possibly can in one sitting…

The recipe is a twist off my Blueberry Lemon Mini Oatmeal Muffins and simply removes the blueberries and lemon from that recipe and replaces with unsweetened cocoa powder and chopped bittersweet chocolate.

I’m planning to continue riffing off this main recipe and see white chocolate macadamia muffins in my very near future! Maybe pumpkin cranberry? Do you have a flavor combo you want me to try?

Save time during the week by making a double batch of muffins to freeze for stressful mornings when you need a quick breakfast or lunchbox treat. Momables has great tips on how to freeze and reheat baked muffins.

If you loved this muffin recipe, then make sure to try my Blueberry Lemon Mini Oatmeal Muffins and Carrot, Coconut and Brown Rice Muffins.

Double Chocolate Mini Muffins

Double Chocolate Mini Muffins

  • Author: Holley Grainger
  • Prep Time: 10 minutes
  • Cook Time: 10 minutes
  • Total Time: 20 minutes
  • Yield: 20 mini muffins 1x


Bite-sized Double Chocolate Mini Muffins guilt-free easily serve as lunchbox treats, breakfasts-on-the-go or after school snacks.



  • ¾ cup whole wheat pastry flour
  • ½ cup uncooked oats
  • 1 Tbsp unsweetened cocoa
  • ¼ tsp cinnamon
  • ⅛ tsp salt
  • ½ tsp baking powder
  • ¼ tsp baking soda
  • ½ cup Greek yogurt (2% is preferred)
  • 1/2 cup applesauce
  • 1 egg
  • ½ tsp vanilla bean paste (or extract)
  • 2 Tbsp brown sugar
  • ½ cup chopped bittersweet chocolate


  1. Preheat the oven to 350 F.
  2. Combine the flour, oats, cocoa, cinnamon, salt, baking powder and soda in a medium bowl.
  3. Combine the yogurt, applesauce, egg, vanilla, and brown sugar in a small bowl.
  4. Pour the bowl with the wet mixture into the bowl with the dry mixture. Mix until just incorporated.
  5. Gently fold in the chopped chocolate.
  6. Pour mixture into a greased muffin pan. Bake at 350 F for 10-12 minutes, or until a toothpick can be cleanly removed from the muffin.
  7. Allow to cool slightly before removing from pan.