Preheat the oven to 350°F. Lightly spray two muffin tins with non-stick spray and set aside.
In a medium bowl, whisk together the pumpkin puree, yogurt, oil, eggs, and brown sugar until they are well-combined and no lumps remain. Set aside.
In large bowl, mix together the flour, baking soda, baking powder, salt, cinnamon, pumpkin pie spice, and chocolate chips. Make a well in the centre of the dry ingredients and pour the pumpkin mixture into it. Stir everything together until just combined.
Fill the prepared muffin tins about 2/3 full. Bake for 18-20 minutes or until a toothpick inserted into the centre of a muffin comes out clean.
Allow to cool in the muffin tins for 5-10 minutes before moving to a wire rack to cool completely. The muffins keep well at room temperature in an airtight container for up to 5 days, or can be frozen for up to 3 months.