Preheat the oven to 350°F and lightly grease or spray a 12-cup muffin tin.
In a large bowl, combine the pumpkin puree, eggs, milk, oil, maple syrup, vinegar, and vanilla and whisk until combined.
In a medium bowl, whisk together the flours, pumpkin pie spice, baking powder, baking soda, and salt.
Add the dry ingredients to the wet ingredients and stir until just combined.
Use a ⅓-cup measuring scoop to divide the batter into the muffin tin. Bake for 18 to 20 minutes, or until a toothpick inserted comes out clean.
Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely.
Notes
To make gluten-free pumpkin muffins, replace both flours with 2 1/4 cupsBob's Red Mill Gluten Free All-Purpose Baking Flour and bake for 22 to 26 minutes.Make these vegan by replacing the eggs with 1/4 cup ground flaxseed mixed with 1/2 cup warm water. Bake for 20 to 22 minutes, or until a toothpick comes out clean.