Preheat the oven to 350 degrees F (175 degrees C). Line a 12-cup muffin tin with paper liners.

Combine flour, baking powder, baking soda, and salt in a bowl. Whisk to combine.

Beat sugar and butter together using an electric mixer in a large mixing bowl until creamy. Add eggs, one at a time, mixing well after each addition. Pour in vanilla extract, almond extract, and coconut extract; mix well. Add flour mixture alternately with buttermilk, mixing until incorporated. Fold in coconut.

Spoon batter into the prepared muffin cups, filling each 2/3 full.

Bake in the preheated oven until a toothpick inserted into the center of a cupcake comes out clean, 15 to 17 minutes. Remove from the oven and transfer to wire racks to cool completely, about 30 minutes.

Beat cream cheese and shortening together using an electric mixer in a mixing bowl until creamy. Slowly add powdered sugar, 1 cup at a time, until creamy. Mix in vanilla extract and almond extract.

Pipe frosting onto cooled cupcakes. Top each with shredded coconut.