Prep your pan and oven. Line a 12-cup muffin tin with paper liners.
Preheat the oven to 425°F (220°C).
Whisk the wet ingredients. In a large bowl, whisk 1 cup pumpkin puree, 2 large eggs, 1/2 cup maple syrup (or honey), 1/4 cup oil, 1 teaspoon vanilla, and 1/3 cup milk until smooth.
Combine the dry ingredients. In a separate bowl, whisk 3/4 cup whole wheat pastry flour, 3/4 cup all-purpose flour, 1 1/2 teaspoons baking powder, 1/2 teaspoon baking soda, 1 1/2 to 2 teaspoons pumpkin pie spice, and 1/2 teaspoon fine sea salt.
Bring it together. Add the dry ingredients to the wet bowl. Stir with a spatula just until no dry streaks remain. If using, fold in 1/2 cup dark chocolate chips or 1/2 cup chopped nuts.
Portion the batter. Divide evenly among the muffin cups, filling each about 3/4 full for a nice dome.
Sprinkle tops with pepitas or a pinch of turbinado sugar if you like.
Start hot for lift. Bake at 425°F for 5 minutes. Without opening the oven, reduce heat to 350°F (175°C) and bake another 13–15 minutes, until a toothpick comes out with a few moist crumbs.
Cool and enjoy. Let muffins rest in the pan 5 minutes, then transfer to a rack. Serve warm or at room temperature.