Prep your pan and oven. Heat oven to 350°F (175°C).
Line a 9x9-inch baking pan with parchment, leaving overhang for easy lifting. Lightly grease the parchment.
Make the crust. In a bowl, whisk almond flour, coconut flour, sweetener, and salt. Stir in melted butter, vanilla, and egg until a moist dough forms.
Press evenly into the prepared pan.
Par-bake the crust. Bake for 10–12 minutes, until the edges are lightly golden. This helps the crust stay crisp under the filling. Set aside while you mix the pumpkin layer.
Whisk the pumpkin filling. In a mixing bowl, whisk pumpkin puree, eggs, sweetener, heavy cream, cinnamon, ginger, nutmeg, cloves (if using), vanilla, and salt until smooth.
Avoid overbeating to limit air bubbles.
Pour and bake. Spread the pumpkin mixture over the warm crust. Bake for 20–25 minutes, until the edges are set and the center still has a slight jiggle.
Make the pecan topping. While the pumpkin layer bakes, melt butter in a small saucepan over low heat. Stir in brown-style sweetener, vanilla, and a pinch of salt until dissolved.
Remove from heat and fold in chopped pecans.
Add the topping. Carefully take the pan out of the oven. Spoon the pecan mixture evenly over the pumpkin layer, spreading gently to avoid tearing the surface.
Finish baking. Return to the oven for 15–18 minutes. The pumpkin layer should be set, and the pecan topping glossy and fragrant.
If the pecans brown too quickly, tent loosely with foil.
Cool completely. Let the bars cool in the pan on a rack for 1 hour, then refrigerate at least 2 hours to fully set. This step makes clean slicing much easier.
Slice and serve. Use the parchment overhang to lift the slab out. Cut into 16 squares with a sharp knife, wiping the blade between cuts.
Top with a tiny pinch of flaky sea salt or a dollop of keto whipped cream, if you like.