I closed my wet flip-flops in a plastic bag for a few months (by accident..). Apparently it was an excellent culture medium for fungi. I can scrub most of it with a dishwashing scrub, but how can I make sure I won't have fungi infection (since there are much more fungi now)?
I would try a water/bleach combination. Saturate the flip-flops. You don't need to use much bleach with the water. Maybe a fourth cup to quart of hot water. Scrub them and put them in the sun