Preheat the oven:
Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners or lightly grease with coconut oil.
Mix dry ingredients:
In a large mixing bowl, whisk together the flour, coconut sugar, baking powder, baking soda, and sea salt.
Combine wet ingredients:
In a separate bowl, mix almond milk, coconut oil (or applesauce), vanilla extract, apple cider vinegar, and unsweetened applesauce until well combined.
Combine wet and dry:
Gradually pour the wet ingredients into the dry ingredients. Stir gently until just combined. Avoid overmixing to keep the muffins fluffy.
Fold in add-ins:
Gently fold in the chopped cherries and dark chocolate chips.
Portion the batter:
Divide the batter evenly among the 12 muffin cups, filling each about ¾ full.
Bake:
Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Cool and enjoy:
Allow the muffins to cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.