Reserve 2 tablespoons of dry vanilla pudding mix. Set aside.
In a medium bowl, whisk together the vanilla pudding mix, 1 ½ cups of whole milk, and chopped bananas until smooth and thickened, about 2 minutes. Cover and refrigerate until ready to use.
Cupcakes
Preheat the oven to 350 F. Line a 12-cup muffin tin with cupcake liners.
In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. Set aside for now.
In a large bowl, combine the melted and slightly cooled butter with the granulated sugar, whisking until well combined.
Add the egg and mix until fully incorporated.
Stir in the mashed bananas and whole milk.
Gradually add the dry ingredients to the wet mixture, mixing until just combined. Don't overmix.
Divide the batter evenly among the cupcake liners, filling each about ⅔ full.
Bake for about 15-20 minutes, or until a toothpick inserted into the center comes out clean.
Let the cupcakes cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Once the cupcakes have cooled, use a small knife or a cupcake corer to remove a small portion of the center of each cupcake, creating a hole for the filling.
Spoon the prepared banana pudding filling into each cupcake cavity. Set aside.
Topping
In a large mixing bowl, beat the softened cream cheese until smooth.
Add the heavy cream, powdered sugar, the reserved 2 tablespoons of vanilla pudding mix, and salt.
Beat the mixture on medium-high speed until stiff peaks form, about 3-4 minutes.
Pipe or dollop the whipped topping over each filled cupcake.
Garnish with additional banana slices and vanilla wafers if desired.
Notes
Vanilla pudding mix: Different brands of instant vanilla pudding will produce lighter or darker yellow vanilla pudding. Instant banana pudding mix will provide a stronger banana flavor.
Whole milk: Whole milk will give you richer, creamier pudding. You can use low-fat or 2% if you prefer. You could also use almond milk or another plant-based milk.
All-purpose flour: Weighing the flour is the most accurate way to measure it. Simply click on "metric" just above the ingredients for the weights. You can also sift or stir the flour well to break it up, lightly spoon it into the measuring cup, and level. Avoid packing the flour as that will give you dry or dense cupcakes.
Salted butter: Unsalted butter + an additional 1/4 teaspoon of salt can be used in place of the salted butter.
Cream cheese: I recommend using full-fat or 1/3-less fat cream cheese. Greek yogurt can be used for a lighter, tangier topping.
Heavy cream: Make sure your heavy cream is very cold before you start your homemade whipped topping. If it’s warm, it won’t for the peaks that you want for the frosting. You can also find more tips for making homemade whipped cream here.