Preheat oven to 350°F. Line a cupcake tin with liners and have a small amount of nonstick spray or oil to coat a spoon.
Make the brownie layer: In the bowl of an electric mixer, beat 1/4 cup softened butter and 3/4 cup granulated sugar until light and fluffy, about 3–4 minutes.
Add 1 large egg and 1 teaspoon vanilla extract to the mixer and mix until combined, scraping down the bowl as needed.
With the mixer on medium speed, add 2/3 cup all-purpose flour, 1 1/2 heaping tablespoons cocoa powder, and a pinch of salt. Mix until just combined.
Gently fold in 1/3 cup mini chocolate chips that have been lightly tossed in flour.
Spoon about 1/2 to 3/4 tablespoon of the brownie batter into each lined cup. Lightly coat the back of a spoon with nonstick spray and press the batter down to form a thin, even brownie layer in each cup. Set the pan aside.
Make the banana bread batter: In a medium bowl, whisk together 1 1/3 cups flour, 1 1/4 teaspoons baking soda, 1/4 teaspoon salt, 1/2 teaspoon cinnamon, and a pinch of nutmeg. Set aside.
In a separate bowl, whisk 1 egg. Add 3/4 cup brown sugar and mix until smooth, then stir in 1 teaspoon vanilla extract.
Add 1/4 cup sour cream and 1/2 cup melted butter to the wet mixture and mix until combined.
Add the dry ingredients to the wet mixture and stir until just combined. Fold in 3 large ripe mashed bananas and mix until the batter comes together; it will be thicker than typical cupcake batter.
Using an ice cream scoop or a 1/4-cup measure, scoop the banana batter into each liner on top of the brownie layer.
Bake at 350°F for 15–18 minutes. Remove from oven and let the cupcakes cool completely in the pan or on a wire rack before frosting.
Make the brown sugar cream cheese frosting: In the bowl of an electric mixer, beat 3/4 cup butter (room temperature) and 8 ounces cream cheese (room temperature) until completely combined and creamy, scraping down the sides as needed.
Add 1 3/4 cups loosely packed brown sugar and 1 1/2 cups powdered sugar. Beat on low speed to combine, then increase to medium speed.
Add 1 tablespoon vanilla extract. Beat the frosting on medium-high speed for 4–5 minutes until very creamy and well combined.
Frost the cooled cupcakes. Note: this frosting is not very thick or sturdy; if you are not serving immediately, refrigerate the frosted cupcakes and remove them up to 30 minutes before serving to soften.