Preheat the oven to 425°F (220°C). Line two 12-cup muffin pans with paper liners, leaving an empty space between each one so no two liners sit side by side — this helps the muffins rise higher.
In a large mixing bowl, whisk together the flour, both sugars, baking soda, salt, cinnamon, and pumpkin spice until evenly combined.
1 3/4 cups all-purpose flour, 3/4 cup sugar, 1/2 cup dark brown sugar, 1 teaspoon baking soda, 1/2 teaspoon salt, 1½ teaspoons cinnamon, 1½ teaspoons pumpkin spice, 1/2 teaspoon of salt
In a separate medium bowl, whisk together the eggs, pumpkin purée, oil, and vanilla until the mixture is smooth and well blended.
2 eggs, 398 ml pure pumpkin puree, 1/2 cup oil, 1 teaspoon vanilla
Gently fold the wet ingredients into the dry mixture until just combined—don’t overmix. Use a scoop to fill each muffin cup nearly to the top.
In a small bowl, beat the softened cream cheese, sugar, flour, vanilla and milk until smooth using a hand mixer or wooden spoon. Mix until well blended. Transfer the filling to a piping bag or a zip-lock bag
142 g cream cheese, 2 ½ tablespoons sugar, 1 teaspoon flour, 1/2 teaspoon vanilla, 2 teaspoons milk
Divide the batter evenly into prepared muffin cups, filling each to the rim.
Snip the tip of the piping bag and pipe the cream cheese into the center of each muffin, using all of the filling for 12 muffins. Insert the tip about ¼ inch below the surface, pressing gently and pulling up in a circular motion to create a small swirl on top. If you have any leftover filling, you can squeeze a little more into the center of each muffin after baking for an extra creamy touch.
Sprinkle chopped pumpkin seeds and coarse sugar (if using) over the top of each muffin, avoiding the cream cheese center.
Bake the muffins at 425°F (220°C) for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 15–17 minutes, or until a toothpick inserted into the muffin batter (not the cream cheese center) comes out clean. Remove the pans from the oven and let them cool for 5 minutes, then transfer the muffins individually to a wire rack to finish cooling.