1 2/3 cups all-purpose flour
1/3 cup unsweetened cocoa powder
1 teaspoon baking powder
1 teaspoon baking soda
1/2 teaspoon fine salt
2 large eggs
3/4 cup packed dark brown sugar
1/2 cup plain whole-milk Greek yogurt
1/2 cup milk (not nonfat)
1/2 cup vegetable oil
1 cup dried cherries
1 cup granola
Arrange a rack in the middle and heat the oven to 400°F. Grease or line a 12-cup standard muffin tin with paper liners.
Whisk the flour, cocoa powder, baking powder, baking soda, and salt together in a large bowl. In a separate medium bowl, whisk together the eggs, sugar, yogurt, milk, and oil until no big lumps of brown sugar remain.
Pour the yogurt mixture into the flour mixture and fold together with a rubber spatula until just combined. Fold in the cherries. Divide the batter among the muffin wells. Sprinkle the muffins evenly with the granola, and press the granola into the batter so it is halfway submerged.
Bake until a toothpick or cake tester inserted into the center of a muffin comes out clean or with just a few moist crumbs, 15 to 20 minutes. Let the muffins cool 10 minutes before removing from the pan. If you greased the pan, run a thin knife around each muffin to loosen it from the pan first. Serve warm or at room temperature.