Preheat the oven to 350 degrees F. Prepare a muffin pan(s) with muffin liners or spray with nonstick cooking spray.
In a small bowl, stir together the drained pineapple pieces and the 3 tablespoons flour. Set aside.
1 20-ounce can crushed pineapple
In a separate bowl, whisk the remaining flour, baking powder, baking soda, cinnamon and salt until well combined. Set aside.
3 cups plus 3 tablespoons all purpose flour, 1 tablespoon baking powder, 1 teaspoon ground cinnamon, 1/2 teaspoon baking soda, 1/2 teaspoon kosher salt
In a third bowl, whisk the oil, sugar, eggs, and vanilla extract until well combined.
1/2 cup vegetable oil, 1/2 cup granulated sugar, 1/2 cup light brown sugar, 2 large eggs, 1 teaspoon vanilla extract
Add the reserved pineapple juice and stir to mix. Then, stir in the flour mixture until just combined.
Fold in the crushed pineapple and half the coconut flakes.
1 20-ounce can crushed pineapple, 1 cup sweetened coconut flakes
Spoon the mixture into each baking cup until the cup is full. Sprinkle the remaining sweetened coconut over the top of each muffin.
Bake in the preheated oven for 18 to 22 minutes for full sized muffins or 12 to 15 minutes for mini muffins, until a toothpick inserted in the center comes out clean.
Remove the muffin pan from oven. Allow muffins to cool for 5-10 minutes in the pan then transfer to a wire rack to cool completely.