Cattle and pig manure contain useful mineral nutrients (N, P, and K) and are therefore used as organic fertilizer. However, excessive applications of manure can cause environmental problems and threaten animal and human health because these materials also hold significant amounts of heavy metals, particularly Cu and Zn. To assess the potential risk due to the increased concentrations of heavy metals (Cu, Mn, Zn, and Cr) in a harvested crop, two maize hybrids were grown in pots on four different soils with three different fertilisers (urea, pig manure, and cattle manure). Both soil and manure characteristics influenced the heavy metal concentrations in the plant shoots. Organic fertilisation strongly interacted with the soils and, in general, reduced the shoot content of Cu, Mn, and Zn. A preliminary assessment of the heavy metal balance of the agricultural systems based on the intensive livestock production and maize cultivation showed that the potential soil enrichment of the long-term application of livestock manure arises mainly from the application of pig slurries that have a high content of Cu and Zn. The time required to apply an amount of metal that is equal to the initial soil content is 60–300 years for Zn and 240–450 years for Cu, depending on the soil type and the initial heavy metal content.