Apply a neutral stone cleaner to the counters. A neutral stone cleaner has a neutral pH that won't damage the stone. Scrub the cleaner over the counter with a soft bristle brush, which will not scratch the limestone. Rub a damp microfiber cloth over the counters and dry with a second cloth. The microfiber absorbs minor dust and debris.
Check the counters for any signs of dirt or stains. If the neutral cleaner left behind any dirty spots, then apply a stronger alkaline-based solution. Leave the cleaner on the stone for at least 10 minutes before scrubbing the stone with your brush. Wipe off the cleaner and stain residue with a damp cloth and repeat if necessary.
Mix the limestone patching compound in a paper cup. Apply the mixture to any cracks or chips in the limestone with a putty knife. While the compound is still soft, gently wipe a damp cloth over the counter. The cloth pulls off any compound sitting on the top of the counter.
Repair scratches in the counter with more of the compound. Apply the compound to a microfiber cloth and gently rub it over the scratches in a circular motion. After the compound dries, rub a dry cloth over the area, rubbing off any excess compound.
Apply the natural stone sealant to the dry limestone with a paintbrush. Carefully paint the clear coating over the stone and let dry overnight. Ensure that the sealant is safe for use in the kitchen, as some products should not touch food.