Heat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease it well.
In a bowl, whisk together both flours, baking soda, baking powder, salt and spices.
In a large bowl, whisk the pumpkin, eggs, brown sugar, oil, milk and vanilla until smooth.
Add the dry ingredients to the wet ingredients and fold with a spatula just until no streaks of flour remain. A few lumps are fine.
Divide the batter evenly among the muffin cups; they will be quite full. Sprinkle with pumpkin seeds if using.
Bake 18–22 minutes, until the tops spring back when pressed and a toothpick inserted in the center comes out clean. Cool in the pan for 5 minutes, then move to a rack.