Preheat oven to 325°F. Line cupcake tin with liners.
Mash bananas in a bowl, set aside.
In a medium bowl, combine almond flour, coconut flour, baking powder, baking soda and salt with a wire whisk. Set aside.
In a large bowl cream butter and 1/4 cup of the sugar with an electric mixer.
Add eggs, bananas and vanilla; beat at medium speed until thick. Scrape down sides of the bowl.
Add flour mixture, then blend at low speed until just combined.
Mix the cream cheese and remaining sugar.
Pour half the batter into muffin pan then add about 2 teaspoons of cream cheese to the center of each muffin and top with the remaining batter; bake on the center rack for 35 to 45 minutes, or until a toothpick inserted in the center comes out clean.