Preheat the oven to 350°F. Keep the gluten-free flour blend and spices near 70°F so they mix without clumping. Whisk the flour, baking soda, ground cinnamon, pumpkin pie spice and fine sea salt for 45 seconds. Use tight clockwise circles and scrape the bowl’s lower edge every 15 seconds. Then lift the whisk twice through the center to break hidden pockets. The mixture should look evenly tan with no white flour streaks or dark spice islands. You’ll smell cinnamon as soon as the spices disperse. Stop after 45 seconds because longer whisking only throws powder from the bowl. Miss this mixing window and one cookie may taste salty while another stays flat. Whisk thoroughly because even leavening prevents bitter pockets.

Cool the melted unsalted butter to 85°F before adding light brown sugar and granulated sugar. Whisk for 60 seconds with firm back-and-forth strokes until the mixture looks glossy and slightly thick. Then add the blotted pumpkin puree, large egg yolk and vanilla extract. Whisk another 45 seconds and scrape the bowl once halfway through. The wet mixture should turn smooth and deep orange with tiny sugar grains still visible. It should smell buttery and warmly spiced, not strongly eggy. My first batch used hot butter, and the dough turned greasy. The cookies spread too far. Go past 90°F and the fat won’t hold the dough properly. Cool the butter because stable fat keeps the cookies thick.

Add the dry mixture to the orange pumpkin base at 70°F in two additions. Fold with a rubber spatula using slow J-shaped strokes for 35 to 45 seconds. Stop when only a few flour streaks remain then fold in 3/4 cup semisweet chocolate chips for 15 seconds. Scrape the bottom once so no dry flour hides underneath. The dough should look thick and scoopable with uneven chocolate chips throughout. Cover it and rest for exactly 20 minutes at 70°F. During that pause, the dough turns less glossy and holds a rounded ridge. Skip the rest and Soft Gluten Free Pumpkin Cookies With Chocolate Chips can spread unevenly and feel gritty. Resting hydrates the flour because dry starch needs time to absorb pumpkin moisture.

Heat the oven to 350°F for at least 15 minutes while the rested dough firms. Scoop 18 portions with a 1 1/2-tablespoon cookie scoop and place nine on each lined sheet pan. Roll each portion once between your palms and press it into a thick 2 1/2-inch mound. Add the remaining 1/4 cup semisweet chocolate chips across the tops. The shaped mounds should stand about 3/4 inch tall with rough edges and uneven chip placement. Finish both trays within 8 to 10 minutes so the first portions don’t warm too much. If the dough slumps before baking, chill the tray for 10 minutes. Flattening too thin makes dry cookies. Thick shaping protects the soft center during baking.

Bake one sheet pan at a time on the center rack at 350°F for 11 to 13 minutes. Rotate the pan front to back at minute 7 without jarring the soft mounds. Remove the tray when the edges look matte and lightly golden but the centers still appear soft. Don’t wait for deep browning across the tops. You’ll smell toasted cinnamon and melted chocolate near minute 10. The tops should look puffed with small cracks and glossy chips. Press one edge gently and it should spring back while the center stays tender. Go past 13 minutes and the pumpkin crumb dries quickly. Pull them early because carryover heat finishes the centers.

Leave the cookies on the hot sheet pan for 10 minutes at about 70°F room temperature. Then move them carefully to a cooling rack and wait another 20 minutes before plating. Use a thin spatula under each cookie because the warm centers bend easily. Finish with 1/2 teaspoon flaky sea salt while the chocolate remains tacky. The cookies should settle slightly and develop firmer golden edges around a soft pumpkin-orange center. Break one cookie after 30 minutes and the crumb should look moist but not wet. Move them sooner and the bottoms can tear. Wait too long to salt and the flakes fall away. Cooling sets the starches because warm gluten-free crumbs are fragile.