The bioavailability and plant uptake of heavy metals (HM), as well as finding the most reliable methods for the prediction of availability, continues to be one of the most crucial problems in agricultural and environmental studies. In agricultural soils from two regions in Kosovo, known for its metal pollution, we collected 60 soil and plant samples (wheat, corn, potatoes, and grass). Heavy metals were extracted from soil with aqua regia (pseudototal concentration), NH4OAc‐EDTA (potential bioavailable), and NH4NO3 (mobile fraction), plant samples were digested with HNO3/H2O2 (microwave assisted extraction). The pseudo total content of Cd, Pb, and Zn showed high value in Mitrovice (mean: Cd–2.92, Pb–570.15, and Zn–522.86 mg kg−1), whereas in Drenas region Ni and Cr showed high value with a mean 258.54 and 203.22 mg kg−1. Also, the potential bioavailability and mobile form of these metals were increased in Mitrovice (mean: Cd–1.59, Pb–217.05, Zn–522.86 mg kg−1, respectively Cd–0.17, Pb–0.64, and Zn–15.45 mg kg−1), compared to Drenas. Cd and Pb were elevated in potato tubers (mean Cd–0.48 and Pb–0.85 mg kg−1). The TF was higher for micronutrients (Zn and Cu) than for non‐essential metals (Cd and Pb). Multiple regression analysis showed a good model for prediction of Cd, Pb and Zn content in plant with significance 99.9%, whereas this model was not significant for Cu, Cr, and Ni. Soil pH played a significant role in the content of Cd and Zn in wheat and potato plants. Clay content also showed significance in Cd concentration in wheat and potato plants, while carbon content was significant for Cd in grass plants, as well as for Zn in wheat and grass plants.