Remove all ripe and overripe fruit from your trees. Female fruit flies lay eggs in the flesh of citrus fruit. Larvae emerge from the eggs and feed on the inside of the fruit. Check for the white larvae when harvesting to confirm an existing population.
Pick up fallen fruit and bury it deeply in the ground or place it in an airtight space until larvae are dead. Kill pupae before adding the fruit to a compost pile; otherwise, the population continues to prosper.
Combine one-part malathion insecticide with three-parts protein hydrolysate compound. Make sure the insecticide is labeled for use on your specific citrus tree. Mix thoroughly and apply to citrus trees where the flies are nesting, two to four times per month, using a high pressure sprayer.
Apply insecticide mixture to nearby border plants that are listed on the label.
Set a commercially-available glass or plastic trap to lure the fruit flies. Tent traps lure flies with a cotton wick and trap them with a sticky floor. Use simple, yellow sticky boards without attractants.