Preheat the oven to 350°F (175°C). Grease two 8-inch round cake pans and line the bottoms with parchment paper rounds.
Whisk all-purpose flour, baking soda, ground cinnamon, ground nutmeg, and salt together in a large mixing bowl.
Whisk granulated sugar, brown sugar, mashed ripe bananas, undrained crushed pineapple, vegetable oil, plain yogurt, and vanilla extract in a separate bowl until thoroughly combined.
Pour the wet mixture into the dry flour bowl and stir gently with a spatula until just combined, then fold in finely chopped pecans.
Divide the cake batter evenly between the two prepared pans and smooth the tops. Bake at 350°F (175°C) for 28 to 32 minutes until a toothpick inserted into the center comes out clean.
Cool the cakes in the pans for 10 minutes, then turn out onto wire cooling racks to cool completely to room temperature.
Beat softened cream cheese and unsalted butter together in a large bowl with an electric mixer until creamy and smooth. Gradually add powdered sugar and vanilla extract, beating on medium-high speed until light, fluffy, and spreadable.
Place one cooled cake layer on a serving stand, spread a generous layer of cream cheese frosting over the top, place the second layer on top, frost the top and sides of the cake, and garnish with toasted chopped pecans.
