Preheat oven to 350°F. Line a 12-cavity muffin pan with cupcake liners, and line a second pan with 4 liners, filling the unused cavities halfway with water (see note 2). Set aside.
Whisk flour, baking soda, baking powder, salt, cinnamon, and nutmeg in a medium bowl and set aside.
In a large bowl, use a hand mixer to beat the butter, brown sugar, and granulated sugar until creamy. Mash enough bananas to make 3/4 cup and blend them into the mixture until smooth. Add the egg, egg yolk, and vanilla, and continue beating until smooth.
Gradually add half the dry ingredients and half the buttermilk to the wet mixture, mixing just until combined. Repeat with the remaining dry ingredients and buttermilk. Be careful not to overmix.
Fill the prepared muffin cups 3/4-full with batter, distributing all the batter evenly among 16 cavities (see note 2). Bake in the preheated oven for 18–22 minutes or until a toothpick inserted comes out clean. Cool in the tin for a few minutes, then transfer to a wire rack to cool completely.
While the cupcakes cool, make the frosting. Cream the room temperature butter and cream cheese until smooth, then mix in vanilla, salt, and cinnamon. Gradually add powdered sugar while mixing on low until smooth. Chill the frosting until ready to use.
Frost the cooled cupcakes with cream cheese frosting and if desired, garnish with a banana chip.
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Notes
Note 1: Make buttermilk by mixing 3/4 cup milk with 3/4 tablespoon vinegar or lemon juice, let sit for 5 minutes before using. Don't use plain milk for this recipe.Note 2: This recipe yields 16 cupcakes, requiring two muffin pans unless you have two 8-cavity pans. Fill empty cavities with water to prevent warping and ensure even heat distribution.Storage: Banana Cupcakes taste better on the second day, with intensified flavors. Store leftovers in an airtight container with a paper towel in the fridge to prevent sogginess, best enjoyed within 3–4 days. Unfrosted cupcakes can be frozen for up to 2 months.