Heat the oven to 325°F and place liners in a cupcake tin.
Mash the bananas in a bowl and put them aside.
In a medium bowl, whisk together the almond flour, coconut flour, baking powder, baking soda, and salt. Set this dry mixture aside.
Using an electric mixer, cream the softened butter with 1/4 cup of the brown sugar in a large bowl.
Add the eggs, mashed bananas, and vanilla. Beat on medium speed until the mixture becomes thick, stopping to scrape down the sides of the bowl as needed.
Add the flour mixture and blend on low speed just until everything is combined.
In a separate bowl, mix the cream cheese with the remaining brown sugar.
Divide half of the muffin batter among the prepared cups. Spoon about 2 teaspoons of the cream cheese mixture into the center of each muffin, then cover with the remaining batter.
Place the pan on the center oven rack and bake for 35 to 45 minutes, until a toothpick inserted into the center comes out clean.