Agroforestry systems aim at increasing the productivity and the environmental sustainability of both crop and animal productions. The integration of small animals such as geese in the vineyard could represent an opportunity to improve farm income and reduce land use for grazing. The main objective of this work was to study the impact of geese rearing in an organic vineyard on the chemical and biochemical properties of the soil and the effect of Copper (Cu) supplied with the fungicide treatments. Furthermore, the amount of Cu in the animal tissues was also investigated. Three experimental areas within the vineyard were selected: High Geese Density (HGD-240 geese ha−1), Low Geese Density (LGD-120 geese ha−1) and Without Geese used as control soil (WG). The results indicated that both HGD and LGD did not affect the main chemical properties of the vineyard soils. LGD increased the amount and the efficiency of the microbial biomass in the upper soil horizons. Moreover, geese through the grazing activity reduced the Cu content in the vineyard soils, accumulating this element in their liver. However, the content of Cu in the breast and drumstick of vineyard geese did not show any significant difference in respect the meat of the control ones.