Prep muffin pans and oven. Preheat oven to 350°F (177°C) and line a 12 cup muffin pan with paper liners, or lightly spray with non-stick spray. Set aside.
Mix the dry ingredients. In a large bowl, whisk the flour together with the baking soda, baking powder, tapioca flour, and salt. Set aside.
Mix the wet ingredients with the sugars. In a medium size bowl, stir the melted coconut oil together with the non-dairy yogurt, both sugars, water, and vanilla extract. Mix until well incorporated.
Combine the wet and dry ingredients together. Pour the wet mixture in with the dry and mix until just combined. Fold in the cherries and chocolate chunks.
Bake. Divide the batter evenly among the muffin cups (the cups should be almost full). Bake for 20-22 minutes or until toothpick comes out (mostly) clean.
Cool. Allow muffins to cool for 15 minutes before removing from cups.
Serve. Enjoy your muffins warm or room temperature.
Happy Eating!