For an old, stubborn stain, the very best way to clean urine from mattress is to apply hydrogen peroxide. As hydrogen peroxide is very strong so dilute it with water and baking soda, before application. Make a mixture of 1 cup hydrogen peroxide, a single cup water and half cup of baking soda. Apply this mixture on the stain and let it sit for about thirty minutes. After half an hour, ... sanding it down to the bare wood. Then, a couple coats of polyurethane will need to be put down to restore the colour you desire and provide a layer of protection against possible damage in the near future.