Remove all sugary fruits and substances from the open areas of the restaurant. Fruit flies are attracted to sugar, so they will migrate toward fruits, sodas, and other sugary foods. Place these items in the kitchen fridge or in another type of storage container.
Wash the kitchen counters, tables and other surfaces in the restaurant daily with dishwashing soap and warm water to prevent sticky residues from building up. Make sure to thoroughly wash surfaces where you notice the fruit flies.
Fill several mugs with orange juice or soda. Using mugs will allow you to create a fruit fly trap that doesn't look unsanitary or out of the ordinary, especially if you need to place it in an area patrons frequent. Place a piece of plastic wrap over each mug and poke a few holes in it with a knife to allow the fruit flies to get in, but not out. Place the mugs near the areas the fruit flies are attracted to. The fruit flies will smell the sweetness of the juice or soda, fly into the mug and get trapped. Make sure to empty the mugs daily.
Remove all garbage from the restaurant on a daily basis. The smell of garbage is sure to attract the fruit flies and will often become a nest. Place a tight lid on any garbage receptacles inside the restaurant.
Attach fruit fly traps to the inside of the garbage can lid or compost bin. These traps are available at home supply stores and general retailers. Garbage receptacles are often breeding grounds for fruit flies, so trapping them there will help to eliminate the problem. Since the trap is inside the receptacle, it won't be obvious to patrons.