Preheat oven to 375 degrees F. Line a 12-cup muffin tin with cupcake liners.
Place all ingredients for the cream cheese filling in a bowl. Use a hand mixer to mix on medium speed until smooth.
8 oz cream cheese, 1 tsp vanilla extract, 1/3 cup granulated sugar
Transfer to a resealable bag or piping bag (without a tip) and chill.
In a large bowl, combine gluten free flour, coconut sugar, baking soda, sea salt, and pumpkin pie spice. Whisk until combined.
1¾ cup gluten free all-purpose flour, 1 cup coconut sugar, 1 tsp baking soda, 1/2 tsp sea salt, 1 tbsp pumpkin pie spice
Add pumpkin puree, eggs, avocado oil, and vanilla extract. Mix until just combined.
1½ cup pumpkin puree, 2 eggs, 1/2 cup avocado oil, 1 tsp vanilla extract
Divide the batter in the prepared muffin tin. Sprinkle the tops with toasted pumpkin seeds.
1/4 cup pumpkin seeds
Cut the tip of the piping bag with the cream cheese filling. Place the tip into each muffin and fill with about 2-3 tbsp of the filling into the batter while pulling up. (You won't use all the filling. Save the rest for after baking to fill the muffins more.)
Bake for 24-28 minutes until a toothpick inserted into the batter part of the muffins comes out mostly clean. If the cream cheese center collapsed, you can add more of the leftover filling.
Cool for 10 minutes, then transfer to a wire rack to cool completely.