Pre-heat your oven to 350 degrees and grease 24 muffin cups or line them with paper liners.
In a large bowl sift together flour, pumpkin pie spice, cinnamon, baking soda, and salt.
With your mixer beat sugar, pumpkin, eggs and oil and water until well combined.
Add the dry ingredients into the wet and mix to combine.
To make the filling: With your mixer beat the cream cheese until it’s light and fluffy. Add in the egg, vanilla and 3 tablespoons sugar and mix to combine.
Fill each muffin cup about 1/4 of the way full with batter. Place about 1 tablespoons cream cheese mixture in the center, then top with remaining batter so that each cupcake is filled about 3/4 of the way.
Bake for 25 to 30 minutes, or until a toothpick inserted into the center comes out clean.
Allow to cool for about 10 minutes before serving. Dust with powdered sugar if you wish.