Preheat oven to 350 degrees F, and line a 9x9 baking pan with parchment paper. Grease any part of the pan that's not covered by the parchment paper.
In a large mixing bowl, add the dry ingredients for the brownie layer: almond flour, cocoa powder, coconut sugar, pumpkin pie spice, baking soda, and sea salt. Stir together.
In another bowl, whisk together eggs, pumpkin puree, ghee, and vanilla extract until combined.
Add wet ingredients to dry ingredients, and fold together until just combined.
Fold in chocolate chips.
Pour the batter into the prepared baking pan, and smooth out into an even layer with a spatula.
In another bowl, stir together all ingredients for the pumpkin swirl layer until fully combined.
Drop small spoonfuls of the pumpkin swirl layer on top of the brownie layer, dispersing it evenly.
Use a knife or the back of a spoon to gently swirl the mixture together, but not too much. Make sure there is still enough of the pumpkin layer on top, or the swirl effect will get blended in with the rest of the batter.
Bake for 30-35 minutes, until a toothpick inserted into the center comes out almost clean.
Cool for 10 minutes, then remove from the pan using the parchment paper. Transfer to a cooling rack, cool for 30 minutes before slicing into 16 squares.
Enjoy immediately, or store covered in the refrigerator for up to a week.