Look first for fruit fly sources in areas where vegetables or fruits are stored but elimination of fruit fly breeding areas is necessary for good management. Fruit flies lay their eggs near the surface of fermenting foods or other moist, organic A better approach, however, is to construct a trap by placing a paper funnel. 7 Smart Ways to Kill Fruit Flies. Compost that mushy produce ASAP that then try one of these effective remedies to banish fruit flies from your kitchen. Every year, I Google 'how to get rid of fruit flies' and every year, I end up using this tried-and-true method.