Line two standard muffin pans with paper baking cups.

Make the filling: In a medium bowl, whisk together the cream cheese and granulated sugar until smooth. Transfer to a piping bag (no tip needed) and snip the end.

Make the muffins: In a large bowl, whisk together the gluten-free flour, almond flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves.

In a medium bowl, whisk together the pumpkin puree, eggs, oil, vanilla, and lemon juice.

Add the pumpkin mixture to the dry ingredients and stir with a rubber spatula until just combined and no dry streaks remain.

Using a kitchen scoop or large spoon, portion the batter evenly into the baking cups, filling each about ¾ of the way full.

Insert the piping bag tip into the center of each muffin and pipe about 2 tablespoons of filling while pulling upward. Sprinkle pumpkin seeds around the edges of each muffin.

Refrigerate the muffins for 20 minutes before baking. Preheat the oven to 375°F.

Bake the muffins for 20-25 minutes, until a toothpick inserted into the muffin (not the filling) comes out clean or with a few moist crumbs.

Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.