Vector-borne diseases pose a growing global health threat, exacerbated by factors such as habitat modification and climate change. Lyme borreliosis, the most common arthropod-borne disease in Europe, is primarily transmitted by the tick Ixodes ricinus. With rising human exposure and no available vaccine, understanding the ecology and epidemiology of the Borrelia burgdorferi species complex is urgently needed for effective control and prevention. However, traditional monitoring approaches face challenges in acquiring large-scale data. Here, we utilize a citizen science initiative, the French CiTIQUE program, to gather georeferenced ticks and Borrelia samples on a broad scale. We investigate the relationship between Borrelia distribution and various factors including vector suitability, climate, ecology, and human activity. Our analysis identifies vector suitability as the primary determinant of Borrelia prevalence. Moreover, we reveal significant spatial heterogeneity in species distribution within the Borrelia burgdorferi complex. We discuss these findings within the context of the current understanding of tick ecology and pathogen dynamics and highlight implications and future challenges for Lyme disease surveillance and prevention.