Preheat your oven to 400°F (200°C). Line a 12-cup muffin pan with paper liners.
In a medium bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, salt, and cinnamon.
In a large mixing bowl, whisk together the honey, coconut sugar, eggs, Greek yogurt, milk, and mashed bananas until smooth.
Gradually add the dry ingredients into the wet ingredients. Stir gently with a rubber spatula until almost combined. Do not overmix.
Fold in the melted oil until just incorporated.
Gently fold in the chocolate chips.
Divide the batter evenly among the prepared muffin cups, filling each nearly to the top.
Bake the Healthy Banana Chocolate Chip Muffins for 18–20 minutes or until a toothpick inserted into the center comes out clean or with a few moist crumbs.
Cool in the pan for 5 minutes before transferring to a wire rack.
Serve warm or allow to cool completely before storing.