Sift flour, baking powder, cinnamon, nutmeg, salt, cloves, and ginger together in a large bowl.
Beat white sugar, butter, and brown sugar together in another bowl using an electric mixer until light and crumbly. Add eggs; beat for 1 minute. Add pumpkin puree, molasses, and vanilla extract; beat until well blended, about 1 minute. Blend in the flour mixture using the mixer or a wooden spoon until dough is sticky and incorporated.
Cover dough with waxed paper; refrigerate for 1 hour.
Preheat oven to 350 degrees F (175 degrees C). Line 2 baking sheets with parchment paper.
Dip your hands into a small bowl of water. Shape the dough into two loaves that are 1 inch high, 3 to 4 inches wide, and 10 inches long, Place each loaf onto a baking sheet; top with pumpkin seeds.
Bake in the preheated oven until bottoms are dry, 20 to 24 minutes. Let cool for 5 minutes. Reduce oven temperature to 275 degrees F (135 degrees C).
Transfer loaves to a flat work surface. Cut each into 10 diagonal slices about 1/2 inch thick. Place sliced biscotti back on the baking sheet.
Continue baking until light golden brown, about 20 minutes. Reduce oven temperature to 200 degrees F (95 degrees C). Continue baking until dry, about 20 minutes more. Transfer to wire racks to cool.