Preheat the oven to 350°F (175°C).
Line a muffin tin with paper liners or grease it.
In a bowl, whisk together the dry ingredients: gluten free flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
In a separate bowl, mix the canned pumpkin puree with brown sugar, granulated sugar, vegetable oil, eggs, and vanilla extract until smooth.
Gradually add the dry ingredients to the pumpkin mixture, stirring until just combined.
Fold in the chocolate chips carefully.
Spoon the batter into the prepared muffin tin, filling each cup about two-thirds full.
Bake for 18-20 minutes or until golden brown.
Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack.