Preheat oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
In a large bowl, whisk together flour, baking soda, salt, and spices.
In another bowl, mix sugar, oil, eggs, pumpkin puree, and vanilla until smooth.
Add dry ingredients to wet ingredients and stir until just combined — don’t overmix.
In a small bowl, beat cream cheese, sugar, and vanilla until smooth and creamy.
Scoop pumpkin batter into lined muffin cups, filling each about ¾ full.
Place the cream cheese filling into a piping bag (or zip-top bag with the tip cut). Pipe about 1 tablespoon of the cream cheese filling directly into the center of each muffin, from the top.
Bake for 18–22 minutes or until a toothpick inserted into the muffin (not the cream cheese) comes out clean. The muffins will rise up around the filling.
Cool in the pan for 5 minutes, then transfer to a wire rack.