How To Get Rid Of Fruit Flies and keep them from coming back I leave a bowl of fruit on the kitchen counter to keep healthy snacks within. While it's nearly impossible to get rid of all traces that a fruit fly is attracted which can be found in any normal grocery store or directly online. If the trap is still buzzing with fruit flies, take the trap outside before removing the . Wash your fresh fruit carefully with water and dry it completely before storing. organic nature but this is the best non-toxic approach to growing healthy fruit.