Preheat an oven to 375 degrees F. Line 18 muffin cups with paper baking cups.
Combine the mix and cocoa powder in a large bowl, and whisk well to dissolve any clumps of cocoa. Set aside.
Whisk together the yogurt, milk, vegetable oil, eggs, and vanilla extract in a bowl until blended. Pour the mixture into the dry ingredients. Stir just until combined. Fold in the cherries and chocolate chips. Spoon into prepared muffin cups, filling three-quarters full.
Bake until a toothpick inserted into centers comes out clean, about 20 to 22 minutes. Cool in pan on wire rack 5 minutes. Remove from pan and cool completely on wire rack. Store tightly covered at room temperature. Reheat briefly or enjoy at room temperature.