This study evaluates the impact of multi-year protection of grapevines using copper-based pesticides on heavy metal content in soil, leaves, and fruit under organic and conventional cultivation methods. Conducted on Solaris, Hibernal, and Muscaris grapevine varieties in north-western Poland, the research highlights significant differences between the two cultivation approaches. In organic vineyards, copper content in soil averaged 10.25 mg/kg, significantly higher than the 9.05 mg/kg found in conventional soils. Manganese levels were also elevated in organic soils (223 mg/kg) compared to conventional ones (299 mg/kg). Conversely, conventional vineyards exhibited higher zinc and lead concentrations, averaging 47.10 mg/kg and 20.34 mg/kg, respectively, versus 43.50 mg/kg and 11.22 mg/kg in organic soils. The organic soils also had higher salinity (46.50 mg/kg) than conventional ones (30.50 mg/kg). The fruits of grapevines in organic cultivation showed higher copper and zinc levels, with the Solaris variety containing 15.01 mg/kg of copper and the Muscaris variety having 11.43 mg/kg of zinc. These levels exceed the commonly encountered ranges of <1 to 10 mg/kg. Lead content in fruits was higher in organic cultivation (2.19 mg/kg) than in conventional cultivation (1.18 mg/kg), occasionally surpassing the critical value for consumable plants (1 mg/kg). Leaves of grapevines from organic vineyards had significantly higher copper and manganese content than those from conventional vineyards, with the Hibernal variety showing the highest levels. These findings underscore the necessity for monitoring and managing heavy metal content in vineyard soils to ensure fruit quality and safety.