Preheat oven to 375 degrees F (190 degrees C). Grease 12 muffin cups or line with paper liners.
Whisk 1 1/2 cup flour, baking soda, baking powder, and salt in a bowl. Beat bananas, 3/4 cup brown sugar, agave syrup, egg, and 1/3 cup applesauce in a separate bowl until thoroughly combined. Stir banana mixture into the dry ingredients to make a smooth batter. Fill muffin cups about 2/3 full of batter.
Mix 1/3 cup brown sugar, 2 tablespoons flour, and cinnamon in a bowl; stir 1 1/2 teaspoons of applesauce into the mixture until it resembles coarse crumbs. Sprinkle topping over muffins.
Bake in the preheated oven until lightly golden brown and a toothpick inserted into center of a muffin comes out clean, 18 to 20 minutes.