Long-term storage of apples faces challenges in maintaining fruit quality and reducing losses from postharvest diseases. Currently the apple industry relies mainly on synthetic fungicides to control postharvest decays. However, the limitations to fungicides such as development of resistance in pathogens, difficulties in developing new fungicides, and their effect on the environment make this practice not sustainable. In addition, growing consumer demand for fungicide free produce and a rapidly expanding organic market necessitate development of more sustainable alternatives to synthetic fungicides. In this chapter we examine various approaches developed for controlling postharvest decays of apples since the introduction of long term storage almost a hundred years ago. They include physical, chemical, and biological treatments. None of the alternative methods has a spectrum of activity as broad as synthetic fungicides; however, when integrated they can provide commercially adequate decay control.