Preheat the oven to 375°F (190°C). Line a 12-cup muffin pan with liners or lightly grease the cups.
In a large bowl, whisk together the flour, cocoa, sugar, baking powder, baking soda, and salt until well combined and no cocoa clumps remain.
In a separate bowl or large measuring cup, whisk the eggs, milk, oil, and vanilla (plus almond extract if using).
Pour the wet ingredients into the dry ingredients.
Stir with a spatula until just combined and no dry streaks show. Do not overmix.
Fold in the cherries and dark chocolate. If using frozen cherries, work quickly to keep the batter cool.
Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle tops with coarse sugar or extra chips if you like.
Bake for 16–20 minutes, or until a toothpick inserted in the center comes out with a few moist crumbs (melted chocolate is fine).
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool further.
They’re great warm when the chocolate is still melty.