Preheat the 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 separate large bowl, whisk together the honey, coconut sugar, eggs, mashed bananas, Greek yogurt, and milk until smooth.
Add the dry ingredients to the wet ingredients and gently fold together until almost combined. Do not overmix.
Fold in the melted oil until incorporated.
Gently stir in the chocolate chips.
Divide the batter evenly among the muffin cups, filling each nearly to the top.
Bake the Healthier Banana Chocolate Chip Muffins for 18–20 minutes, or until golden and a toothpick inserted into the center comes out clean or with a few moist crumbs.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack.
Serve warm or at room temperature.