Prepare the dough by combining pumpkin puree, eggs, granulated sugar, and vanilla extract in a large mixing bowl. Blend until smooth.
In another bowl, whisk together baking soda, ground cinnamon, ground nutmeg, ground ginger, salt, almond flour, and coconut flour. Gradually add to the pumpkin mixture and stir gently until just combined.
Prepare the cream cheese filling by beating together softened cream cheese, unsalted butter, powdered sugar, and vanilla extract until smooth.
Pour the pumpkin batter into a prepared jelly roll pan and bake until set, about 15-20 minutes. Let cool in the pan for 5 minutes.
Invert the cake onto a powdered sugar-dusted towel, roll it up, and let it cool completely.
Unroll the cake, spread the cream cheese filling evenly, and roll it back up. Wrap in plastic wrap and refrigerate for at least 1 hour before slicing.