Preheat oven to 425°F. Line a 12 count muffin pan with liners and spray them nonstick cooking spray and set aside.
In a large mixing bowl, whisk the eggs, brown sugar, granulated sugar, pumpkin puree, melted butter and vanilla until combined.
2 large eggs, 3/4 cup light packed brown sugar, 1/4 cup granulated sugar, 1 cup pumpkin puree, 3/4 cup unsalted butter, 1 teaspoon vanilla extract
In a medium bowl, whisk together the gluten-free flour, baking powder, baking soda, salt and pumpkin pie spice. Add the dry ingredients to the wet ingredients and gently whisk until just combined, being careful not to over mix. Add the chocolate chips, reserving a few for the tops of the muffins, and fold in gently. The batter will be thick. Let the batter rest for 10 minutes.
1 3/4 cups 1:1 gluten free flour, 1 teaspoon baking powder, 1 teaspoon baking soda, 1/2 teaspoon salt, 2 teaspoons pumpkin pie spice, 1 cup semi-sweet chocolate chips
Scoop the muffin batter out of the bowl and fill each muffin tin all the way full, almost overflowing. Add the reserved chocolate chips to the top of the unbaked muffins.
Bake the muffins 5 minutes at 425°F then, keeping the muffins in the oven, reduce the oven temperature to 350°F. Bake for an additional 15-18 minutes, or until a toothpick inserted in the center comes out clean.
Remove the muffins from the oven and allow to cool in the pan for 5-10 minutes then transfer to a wire rack to cool completely. Store in an air tight container at room temperature for up to 5 days or in the freezer for up to 3 months.