1. Preheat oven to 375 degrees Fahrenheit (190 degrees Celsius).
2. Place 1/2 cup chocolate chips, soy milk, and oil in a microwaveable bowl and microwave until chips are melted and mixture is smooth. Set aside.
3. In a large bowl, combine flour, sugar, baking powder, cinnamon, pecans, and remaining two tablespoons chocolate chips.
4. Combine egg, vanilla extract, melted chocolate chip mixture and applesauce in small bowl; stir into flour mixture just until moistened.
5. Prepare muffin tins by greasing and filling with cupcake holders. Spoon the batter into the cupcake holders, filling 3/4 full. Sprinkle with topping. Bake 20–25 minutes.