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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.
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.
Add pumpkin puree, eggs, avocado oil, and vanilla extract. Mix until just combined.
Divide the batter in the prepared muffin tin. Sprinkle the tops with toasted 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. (If you don't use all the filling, you can add more after baking to make the muffins fuller.)
Bake for 24-28 minutes until a toothpick inserted into the batter part of the muffins comes out mostly clean.
Cool for 10 minutes, then transfer to a wire rack to cool completely.