Mix the pumpkin puree, applesauce, brown sugar, white sugar, eggs, and vanilla in a stand mixer with the paddle attachment on low setting for 1 minute.
Add flour, pumpkin pie spice, baking powder, and salt to the wet ingredients and mix until ingredients are combined, about 2 minutes.
Fold the chocolate chips into the batter.
Scoop muffin batter into the muffin pans, filling each about 2/3 full.
Bake for 20 minutes or until a toothpick inserted into the center of the muffins comes out clean.
Remove muffins from the oven and cool on a cooling rack for at least 15 minutes.