Preheat oven to 350 degrees F (180 degrees C). Place oven rack in the middle of the oven. Line 8 standard muffin cups with paper liners.
In a medium bowl, whisk together all dry ingredients (whole wheat flour, sugar, cocoa powder, baking powder, baking soda and salt).
In another medium microwavable bowl, add 3 ounces (⅓ cup + 2 tablespoons) chocolate chips. Microwave on high for 1 minute 30 seconds, stirring every 30 seconds, until melted.
Remove from microwave and whisk in all wet ingredients. First whisk in mashed avocado until very smooth and then followed by greek yogurt, egg and vanilla extract. Whisk until very smooth. Then add dry flour-sugar mixture and whisk until smooth.
Stir in remaining 2 ounces (¼ cup + 1 tablespoon) chocolate chips. Divide batter between the 8 muffin cups.
Bake for 22-24 minutes, until a tooth pick inserted in the middle of a muffin comes clean (Don’t let it over bake).
Place pan on a wire rack to cool completely.