Systematic management of plant canopy is an important tool for optimizing economic and environmental outcomes by integrating food crops and cash crops and in tree crop production systems. It can be an effective tool in the attainment of food security through diversification of risk and income by small scale farmers. Many smallholder coffee farmers often face a difficult choice between cash (tree) crops and food crops on their limited landholdings, while an ideal situation would be a capacity to grow both crops concurrently. In their natural ecosystems, these bushy crops grow under large trees, and hence, in commercial farms both coffee and cocoa are grown under shade trees in polyculture farming systems. These systems involve the farmers growing these bushy crops grown under larger shade trees, and then growing mostly seasonal food crops as groundcover. In this short review, we considered how management of the upper (shade tree) and middle (coffee) canopies influence yields of the fruit tree and food crops and hence productivity of the whole farm. We identified several desirable features of shade trees needed to optimise coffee productivity to include minimal management requirements, persistence, short and open canopy, and deciduous phenology, amongst others. We present examples of where growing food crops with coffee in polyculture system generally had minimal impact on the yields of coffee beans, but actually often increased net economic yield by up to 400% over that obtained from farms growing coffee alone.