While the pepitas are in the oven, prepare the dry mix. In a medium bowl, combine the flour, salt, baking powder, baking soda, cinnamon, cloves, ginger and nutmeg. Whisk to combine; set aside.
Using an ice cream scooper or a spoon, completely fill each muffin tin to the top with batter. Divide the toasted pepitas evenly and sprinkle on top of each muffin.
Press gently to adhere the seeds to the batter. Bake in the preheated 350 degree oven for 30-35 minutes until a cake tester or toothpick inserted into the center comes out clean.
Let the muffins rest in the pan for 5 minutes (as this is still part of the baking process) and then turn them out onto a wire rack to cool for an additional 10 minutes.
These muffins are best enjoyed on the day they are baked. They can be stored in an air tight container for up to 2 days or in the refrigerator for up to 5 days.