Preheat the oven to 425 degrees F. Line a 12-cup muffin tin with muffin liners.
In a large mixing bowl, combine the all-purpose flour, wheat flour, cinnamon, nutmeg, allspice, ginger, cloves, baking soda, baking powder, and salt. Whisk together until fully combined and set aside.
Add all the wet ingredients to a blender or food processor - the pumpkin puree, cottage cheese, eggs, oil, honey or maple syrup, and vanilla extract. Blend until completely smooth.
Pour the wet mixture into the dry ingredients. Stir until just combined. Be careful not to overmix.
Let the batter rest for 10 minutes. This step helps hydrate the flour and gives you taller, better-textured muffins.
Divide the batter evenly among the 12 muffin tins.
Bake at 425 degrees F for 5 minutes, then reduce the heat to 350 degrees F and bake for an additional 12-15 minutes, or until a toothpick inserted in the center comes out clean.
Remove from the oven and let cool before enjoying.