Line a standard muffin pan with paper baking cups.
In a large bowl, whisk together the gluten-free flour, almond flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg and cloves.
In a medium bowl, whisk together the pumpkin puree, eggs, oil, vanilla and lemon juice.
Add the pumpkin mixture to the dry ingredients and stir with a rubber spatula until just combined and no dry flour streaks remain. Fold in the chocolate chips, if using.
Using a kitchen scoop or large spoon, portion the batter evenly into the prepared muffin pan.
Refrigerate the muffins for 20 minutes before baking. Preheat the oven to 425°F.
Bake the muffins for 10 minutes at 425°F, then reduce the oven temperature to 375°F and continue to bake for 10-15 minutes, until a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.