Preheat oven to 350°F (175°C). Line a 22-cup muffin tin with paper liners.
In a large bowl, whisk together all-purpose flour, whole wheat flour, sugar, baking soda, salt, cinnamon, nutmeg, and ginger.
In a medium bowl, whisk together oil, eggs, and vanilla extract. Stir in mashed bananas and drained crushed pineapple until well combined.
Pour the wet ingredients into the dry ingredients and fold gently until just combined. Do not overmix. Fold in the chopped pecans.
Spoon the batter evenly into the prepared muffin cups, filling each about two-thirds full.
Bake for 20-23 minutes, or until a wooden toothpick inserted into the center of a cupcake comes out clean.
While the cupcakes are baking, prepare the frosting. In a medium bowl, beat together cream cheese, powdered sugar, and vanilla extract until smooth and creamy.
Let the cupcakes cool in the muffin tin for 5-10 minutes before transferring them to a wire rack to cool completely.
Once the cupcakes are completely cool, frost them generously with the cream cheese frosting. Garnish each cupcake with a pecan half.
Notes
These cupcakes are best enjoyed at room temperature. Store leftover frosted cupcakes in an airtight container in the refrigerator for up to 3 days.