Seal the onyx countertop with an impenetrable food-safe countertop seal. According to Bob Vila, Miracle Sealant and Aqua Mix are two trusted companies with high quality seals. Follow the directions on the package and re-apply the seal when water no longer beads on the surface. This will help prevent acids from etching the surface.
Use a cutting board while preparing foods. This will provide a layer of protection between the countertop and any foods that may etch and ruin the surface of the onyx.
Blot any spills immediately from the surface of the countertop. Do not wipe the spill or the size of potential harm will widen. Leaving spills, will, again, cause harm to the onyx surface, especially if they are acidic in nature.
Clean the countertops thoroughly with a safe cleaner and a soft cloth. Many cleaners are too acidic for onyx. Often "green" products offer a balanced pH for cleaning. Look for a "stone safe" marking on the cleaning product to be sure.