The cestode, Echinococcus multilocularis, is one of the most threatening parasitic challenges in the European Union. Despite the warming climate, the parasite intensively spread in Europe's colder and warmer regions. Little is known about the expansion of E. multilocularis in the Balkan region. Ordinary least squares, geographically weighted and multi-scale geographically weighted regressions were used to detect global and local drivers that influenced the prevalence in red foxes and golden jackals in the southwestern part of Hungary. Based on the study of 391 animals, the overall prevalence exceeded 18% (in fox 15.2%, in jackal 21.1%). The regression models revealed that the wetland had a global effect (β = 0.391, p = 0.006). In contrast, on the local scale, the mean annual precipitation (β = 0.285, p = 0.008) and the precipitation seasonality (β = − 0.211, p = 0.014) had statistically significant effects on the infection level. The geospatial models suggested that microclimatic effects might compensate for the disadvantages of a warmer Mediterranean climate. This study calls attention to fine-scale analysis and locally acting environmental factors, which can delay the expected epidemic fade-out. The findings of our study are suggested to consider in surveillance strategies.