Heat your oven to 350 degrees F. Spray a 24-cup mini muffin tin thoroughly with nonstick cooking spray, getting into the edges of each cup. Mini muffin liners work too, though greasing directly gives cleaner edges on the mini size.

Make the cream cheese topping. Beat the softened cream cheese, 3 tablespoons granulated sugar, and 1 teaspoon vanilla together until smooth and fluffy, about 1 minute with a hand mixer. Spoon the mixture into a small zip bag, press out the air, and seal it. Set aside at room temperature while you make the batter. Do not refrigerate it this time since you want it soft enough to pipe easily into small cups.

In a large bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon until evenly combined.

In a second large bowl, whisk the pumpkin puree, eggs, brown sugar, oil, milk, and vanilla until smooth. Pour the wet mixture into the dry ingredients and fold with a rubber spatula until just combined. Stop as soon as no dry flour streaks remain. Overmixing makes mini muffins tough.

Fill each mini muffin cup about 2/3 full with batter, roughly 1 tablespoon each. A small cookie scoop makes this faster and more even. Snip a small corner off the zip bag holding the cream cheese mixture. Pipe a rounded teaspoon of cream cheese filling right onto the center of each filled cup. It should sit on top, not mixed in.

Bake on the center rack for 12 to 14 minutes. The tops will look lightly golden around the edges and the cream cheese topping should be just set with no jiggle when you gently shake the pan. A toothpick inserted into the pumpkin batter beside the topping should come out with just a few moist crumbs, not wet batter.

Remove the pan from the oven and let the muffins sit for exactly 5 minutes in the pan. Do not leave them longer than that. Mini muffins trap steam on their bottoms quickly and the undersides will turn soft and gummy if they sit in the hot pan too long. Turn them out onto a wire rack and let them finish cooling for at least 10 minutes before packing or eating.