Preheat your oven to 350°F (175°C) and line a muffin tin with cupcake liners.
In a large bowl, mix together the honey (or maple syrup), Greek yogurt, applesauce, almond milk, and vanilla extract until well combined.
In a separate bowl, whisk together the whole wheat flour, baking powder, baking soda, and salt.
Gradually add the dry ingredients and cocoa powder to the wet ingredients, stirring until just combined. Be careful not to overmix.
Gently fold in the pitted cherries.
Spoon the batter evenly into the cupcake liners, filling each about 2/3 full.
Bake in the preheated oven for 18-20 minutes or until a toothpick inserted into the centre of a cupcake comes out clean.
Remove from the oven and let the cupcakes cool in the muffin tin for a few minutes, then transfer them to a wire rack to cool completely.
In a separate bowl, whip the cream or yoghurt until thick and fluffy.
Once cooled, top each cupcake with a dollop of whipped coconut cream or Greek yogurt and garnish with additional cherries and shredded dark chocolate, if desired.