Environmental contamination by heavy metals remains a persistent ecological concern in regions with a history of mining and metallurgical activity. In Kosovo, historical Pb-Zn-Cd smelting in the Mitrovica region and ongoing ferronickel production in Drenas provide a relevant framework for distinguishing between legacy and active sources of metal pressure. Although primary lead production ceased in 2000, legacy contamination may persist in soils and enter the food chain. This study investigated the spatial distribution of Pb, Cd, Zn, Ni, and Cu in honey samples (n = 24) collected from different local sampling points in industrial, rural, and mountainous regions of Kosovo. Element concentrations were determined using ICP-MS in an ISO/IEC 17025 accredited laboratory, and statistical evaluation was performed using Welch’s robust ANOVA followed by Games-Howell post-hoc comparisons. Significant spatial differences were observed for Pb and Ni (p < 0.001) and for Cd (p < 0.001 in Welch’s robust test), whereas Zn and Cu did not differ significantly among zones. Elevated Pb concentrations near historically industrialized areas indicate the persistence of legacy contamination, whereas the distribution of Ni reflects the combined influence of ongoing industrial activity and local environmental variability. All measured concentrations remained below the current European Union maximum level established for Pb in honey. The results demonstrate that honey can effectively differentiate between legacy contamination associated with historical Pb-Zn smelting and ongoing industrial metal emissions from ferronickel production. This study provides the first spatially resolved assessment of heavy metal pressure in Kosovo using honey as a bioindicator, contributing to regional environmental monitoring and food safety evaluation.