Preheat the oven to 350°F. Line a standard 12-cup muffin pan with paper liners.
In a medium bowl, whisk together the flour, baking soda, cinnamon, ginger, nutmeg, cloves, and salt. Set aside.
Add the pumpkin puree, cottage cheese, eggs, brown sugar, granulated sugar, vegetable oil, and vanilla to a blender.
Blend just until smooth and creamy and no obvious cottage cheese curds remain.
Pour the blended pumpkin mixture into a large mixing bowl.
Add the dry ingredients and gently fold with a rubber spatula just until no dry streaks of flour remain. Do not overmix.
If using chocolate chips, chopped walnuts, or chopped pecans, fold in up to 3/4 cup when only a few streaks of flour remain.
Divide the batter evenly among the 12 prepared muffin cups, filling each approximately three-quarters full.
If desired, sprinkle additional chocolate chips, chopped nuts, or pumpkin seeds over the tops.
Bake at 350°F for 20–24 minutes, until the tops are set and spring back gently when touched. A toothpick inserted into the center should come out clean or with a few moist crumbs, not wet batter.
Let the muffins cool in the pan for about 10 minutes.
Transfer the muffins to a wire rack and allow them to continue cooling before serving.