Preheat the Oven – Preheat to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners.
Make the Cream Cheese Filling – Beat together the cream cheese, granulated sugar, vanilla extract, and flour with a hand mixer for about 2 minutes until smooth.
Mix the Dry Ingredients – In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice. Set aside.
Mix the Wet Ingredients – In a medium bowl, whisk the brown sugar, granulated sugar, eggs, pumpkin, melted butter, milk, and vanilla extract until combined.
Combine Wet and Dry – Pour the wet ingredients into the dry ingredients and stir until just combined. Avoid over-mixing to keep the muffins tender.
Fill the Muffin Pan – Use a cookie scoop to evenly divide the batter into the 12 muffin cups, filling almost to the top for bakery-style domes.
Add the Cream Cheese Filling – Transfer the filling to a piping bag or zip-top bag with the corner cut off. Insert the tip halfway into each muffin, squeeze as you lift, and fill the center until it reaches the top. You may have a little bit of leftover filling.
Add the Pumpkin Seeds – Sprinkle pumpkin seeds around the edges of each muffin, keeping the cream cheese center visible.
Bake – Bake at 425°F (218°C) for 5 minutes. Without opening the oven, reduce the temperature to 350°F (177°C) and bake for another 12 -15 minutes, for a total bake time of around 20 minutes.
Cool – Let muffins cool in the pan for 10 minutes before transferring to a wire rack to cool completely.
Store – Cover tightly and store at room temperature for up to 2 days, or refrigerate for up to 1 week.