Preheat the oven to 350°F (175°C). Grease a 9″x5″ loaf pan or line it with parchment paper.
In a medium bowl, combine the all-purpose flour, whole wheat pastry flour, baking powder, baking soda, salt, cinnamon, ginger, and cloves. Stir until evenly mixed.
In a large bowl, whisk together the applesauce, maple syrup, molasses, eggs, vanilla, and milk until smooth.
Add the dry ingredients to the wet ingredients and gently stir until just combined. Avoid overmixing to keep the loaf light and tender.
Pour the batter into the prepared loaf pan and bake for 45–50 minutes, or until a toothpick inserted in the center comes out clean. If the top starts to brown too quickly, cover with foil to prevent burning.
Let the loaf cool in the pan for 15–20 minutes before removing it.
To make the frosting, combine the cream cheese, butter, powdered sugar, and maple syrup in a bowl or stand mixer. Whisk until smooth and fluffy. Spread the frosting over the cooled loaf and serve.