The long-term variability of total Cu content from fungicides applied in a certified wine region of Spain (La Rioja) and of other metals (Cd, Cr, Ni, Pb, and Zn) was evaluated in three young vineyard soils and subsoils unamended and amended with spent mushroom substrates (SMS) over a 3-year period (2006-2008). SMS is a promising agricultural residue as an amendment to increase the soil organic matter content but may modify the behaviour of metals from pesticide utilisation in vineyards. Fresh and composted SMS was applied each year at a rate of 25 t ha(-1) (dry-weight). Copper concentrations in the three unamended soils were 21.2-88.5, 25.5-77.1, and 29.4-78.4 mg kg(-1). They exceeded natural Cu concentrations of the region and reference sub-lethal hazardous concentration for soil organism. The concentrations of Cd, Ni, Pb, and Zn were largely below the sub-lethal limits. Thus, although Cu levels were lower than those of established vineyards, vine performance, and productivity might be affected. The variation in behaviour between different amendments for each soil was high, so a generic conclusion could not be drawn. The amendment practice seemed to have caused temporarily Cu mobilization respect to untreated soils. Total zinc concentrations fall within the range of the natural soil of La Rioja and were significantly affected (p < 0.05) especially by fresh state SMS addition, with increasing up to 75% respect to untreated specimen. The results indicated a build-up of fresh sites for metal retention at both surface and subsurface level, although no accumulation of metals was observed in the short-term period. However, the benefit for soils and the negative effects need to be monitored in the long run.