Preheat your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease it.
In a large bowl, whisk together the flour, oats, baking soda, baking powder, salt, cinnamon, ginger, nutmeg, and cloves.
Set aside.
In a blender or food processor, blend the cottage cheese until mostly smooth. This step ensures a silky batter with no visible curds.
In a separate bowl, whisk the pumpkin puree, blended cottage cheese, eggs, maple syrup, brown sugar, oil, and vanilla until well combined.
Pour the wet mixture into the dry ingredients. Stir with a spatula until just combined. Do not overmix; a few small lumps are fine.
Fold in any add-ins like chocolate chips or nuts.
Let the batter rest for 5 minutes to hydrate the oats and develop a tender crumb.
Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle pumpkin seeds on top if using.
Bake for 18–22 minutes, or until a toothpick inserted in the center comes out clean or with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. The muffins will set as they cool.