Sand the floor using 200-grit sandpaper in a floor sander until the surface is dull and not shiny.
Vacuum up the stone dust. Mop the floor with stone cleaner and remove any oily or greasy spills on the floor. Allow the flagstone floor to dry completely.
Paint in between the flagstones with a paintbrush. You can use the same color paint or a different color to set off the stones. Get into every nook and cranny with the brush.
Pour paint into a tray, dip a roller into the paint and roll it over the top of the flagstones until they are covered with paint.
Allow the floor to dry for at least 24 hours before you walk on it.