This study assessed both the soil and litter copper (Cu) levels and their relationships with soil microbial activity, in fruit-tree production areas of central Chile where Cu-based pesticides are intensively sprayed. Samples of soil (0–20 cm depth) and litter from a number of selected orchards (kiwi, table grape, plum, and cherry) were collected and analysed for their Cu content and C-induced soil microbial activity. Results showed that the mean total soil Cu level was 225 mg/kg and soluble soil Cu was less than 0.01% of total soil Cu, as expected from pH values of study soils (range of 6.33 to 7.93). However, leaf litter Cu content was 3–7 times higher than in soil (mean of 681 mg/kg). Despite the soil and leaf litter Cu concentrations, no effect was observed on the C-induced soil microbial activity. We conclude that leaf litter exerts a protective role, preventing the entry of Cu into the soil and thus soil microbial toxicity.