Preheat oven to 325°F. Line a muffin pan with paper liners and place on the center oven rack.
Peel and mash the very ripe bananas in a medium bowl until mostly smooth; set aside.
In a medium bowl, whisk together the almond flour, coconut flour, baking powder, baking soda, and salt; set aside.
In a large bowl, use an electric mixer to cream the softened butter with 1/4 cup of the brown sugar on medium speed until light and fluffy.
Add the eggs, mashed bananas, and vanilla extract to the butter-sugar mixture and beat on medium speed until combined and slightly thickened. Scrape down the sides of the bowl as needed.
Add the flour mixture to the wet ingredients and blend at low speed just until the batter is combined; do not overmix.
In a small bowl, beat the cream cheese with the remaining brown sugar until smooth.
Assemble muffins: Pour half of the batter into the lined muffin cups, filling each cup about halfway. Spoon about 2 teaspoons of the cream cheese mixture into the center of each cup. Top each with the remaining batter, covering the cream cheese and filling each cup about three-quarters full.
Bake on the center rack for 35 to 45 minutes, or until a toothpick inserted into the cake portion (not directly into the cream cheese center) comes out clean and the tops are set.
Remove the pan from the oven and let the muffins cool in the pan for 5–10 minutes, then transfer muffins to a wire rack to cool completely.