Preheat your oven to 350°F (175°C). Line a muffin pan with paper liners.
In a medium bowl, whisk together the all-purpose flour, baking soda, baking powder, and salt until well combined. Set aside.
In a large bowl, mash the bananas and mix in the granulated sugar and brown sugar. Beat in the egg, vegetable oil, and vanilla extract until smooth.
Gradually add the flour mixture to the banana mixture, stirring just until no lumps remain. Fold in the chopped pecans.
Fill each muffin cup ¾ full with the batter.
In a separate medium bowl, beat the softened cream cheese until smooth. Add in the granulated sugar, egg yolk, and vanilla extract, and beat until well combined. If the cream cheese mixture is too thick, add 1-2 teaspoons of milk to reach the desired consistency.
Drop about 1 tablespoon of the cream cheese mixture on top of each muffin. Use a toothpick to gently swirl the cream cheese into the muffin batter. It won’t look perfectly smooth, but it will bake beautifully.
Bake the muffins for 16-18 minutes, or until a toothpick inserted into the center comes out clean.
Serve the muffins fresh. Store any leftovers in an airtight container in the refrigerator. These muffins are best enjoyed at room temperature or slightly chilled.