High soil copper may result in adverse effects on natural and agricultural systems. Copper-based pesticides have long been used for control of microbial diseases on fruit tree productive systems. Although copper is relatively safe from a human health management point of view, it can be accumulated in agricultural soils, affecting soil microbiota and litter degradation. The purpose of this review was to collect the available information to critically discuss the role that litter may play in fruit tree productive systems, in terms of copper incorporation into the soil, where this element is used as a pesticide. To achieve this objective, we focused our review on (1) soil contamination by copper-based pesticides in fruit production systems, (2) soil copper behavior, (3) effects of copper contamination on soil organisms, and (4) copper-litter relation in soil. From this review, we can suggest that (1) litter is the main sink of metals coming from atmospheric fallout because it is a good complexing agent of cations, (2) litter decomposition depends on its quality and in soil microbial activity, and (3) soil and litter microbial activity is negatively affected by soil copper enrichment. Thus, under uncontrolled applications of copper-based pesticides in fruit tree productive systems, copper soil enrichment will generate a decrease in microbial activity, diminishing litter breakdown and decreasing dissolved organic carbon formation. This process will also decrease the soluble copper incorporation into the soil; however, this assumption remains unevaluated.