Preheat the oven to 350 degrees F (175 degrees C). Grease a 9-inch square baking pan.
Blend pumpkin puree, 1 1/2 tablespoons coconut oil, 3 tablespoons orange juice, nutmeg, and cinnamon together in a bowl. Refrigerate pumpkin swirl until needed.
Combine hot water and flaxseed meal in a small bowl. Stir and let soak for about 5 minutes.
Combine flaxseed mixture, almond flour, sugar, 3 tablespoons orange juice, 1 1/2 tablespoons coconut oil, and vanilla extract in a blender and process. Transfer to a bowl. Stir melted chocolate, pecans, baking powder, salt, and pepper into brownie mixture.
Spread brownie mixture into the prepared baking pan. Spread pumpkin swirl on top. Run a knife through the mixture to create a pretty marbled look.
Bake in the preheated oven for 30 minutes. Cover the baking pan with aluminum foil and return to the hot oven. Bake until brownies are set, about 20 minutes more. Cool completely before slicing and serving, about 30 minutes. Store in the refrigerator.
