Preheat oven to 400 degrees F (200 degrees C). Spray 18 muffin cups with cooking spray or line with paper liners.
Whisk all-purpose flour, whole wheat flour, cinnamon, ginger, baking soda, nutmeg, allspice, and salt together in a bowl; form a well in the center.
Stir brown sugar, pumpkin, soy milk, oil, molasses, eggs, and vanilla extract together in a separate bowl until well mixed. Pour brown sugar mixture into the well of the flour mixture and stir until batter is just combined; fold in chocolate chips. Spoon batter into the prepared muffin cups.
Bake in the preheated oven until a toothpick inserted into the center of a muffin comes out clean, about 15 minutes. Remove muffins from pan immediately and cool completely on a wire rack.
