Spread the pumpkin puree on a double layer of paper towels and press another towel on top to blot out as much moisture as you can. This step is the secret to chewy cookies instead of cakey ones.
In a medium bowl, whisk together the almond flour, pumpkin pie spice, baking soda, xanthan gum and salt.
In a large bowl, whisk the melted butter and brown sugar substitute until combined. Add the blotted pumpkin, egg yolk and vanilla and whisk until smooth and glossy.
Stir the dry ingredients into the wet ingredients until a soft dough forms, then fold in the chocolate chips. Cover and chill the dough for 20 minutes.
Preheat the oven to 350°F and line a baking sheet with parchment paper. Scoop the dough into 14 balls, place them 2 inches apart and flatten each to about 1/2 inch thick.
Bake for 11 to 13 minutes, until the edges are golden and the centers still look slightly soft. Sprinkle with flaky sea salt right away.
Let the cookies cool on the baking sheet for at least 15 minutes. They will be very soft out of the oven and set into a chewy texture as they cool.