Preheat the oven to 350 degrees F (175 degrees C). Spray a 12-cup muffin tin with cooking spray, or line with paper liners.
Combine flour, brown sugar, white sugar, cinnamon, baking soda, and salt in a large bowl.
Combine pumpkin puree, mashed banana, yogurt, butter, eggs, and vanilla extract in a large mixing bowl; beat with an electric mixer until well combined. Add dry ingredients and mix until just combined. Scoop batter into the prepared muffin cups.
Mix pecans, sugar, and cinnamon together in a small bowl. Spoon or sprinkle on top of each muffin.
Bake in the preheated oven until a knife inserted into the center comes out clean, 20 to 25 minutes.