Preheat oven to 350°. Line a 12-cup muffin pan with paper baking cups.
Combine first 5 ingredients in a large bowl, stirring well. Whisk eggs with butter and orange zest in a separate large bowl. Stir in pineapple and bananas. Add egg mixture to flour mixture, stirring until well blended.
Pour batter evenly into prepared cups. Bake 20 minutes or until toothpick inserted in center of cupcakes comes out clean. Cool in pans 5 minutes, and then place on wire rack to cool completely.
Spread Cream Cheese Frosting over cupcakes. Sprinkle evenly with coconut flakes.