Recent climate change has caused pristine Arctic winter atmosphere to experience a strong variation in ambient temperature, leading to significant alterations in polar wind patterns and thereby, perturbation in airborne microbial community. Present study focuses on investigating atmospheric transported microorganisms via wind and clouds, altering polar microbial diversity in polar dark winter nights at Ny-Ålesund, Svalbard (78.9° N, 11.9°E), as part of the first Indian winter-time Arctic expedition conducted from 19th January to 12th February 2024. Average wintertime Arctic airborne cell concentration is noticed to be 1.5 ± 0.5 × 104 per m3. During the study period, Ny-Ålesund experiences a change in locally observed winter wind patterns from northerly winds to southerly winds. Significantly distinct clusters of microbial diversity are noticed corresponding to polar-influenced northerly wind (PW), southerly wind (SW) and precipitation (AP) over Ny-Ålesund. Microorganisms are primarily transported to Arctic by clouds, which contribute approximately one-third of bacterial and fungal genera through precipitation. In contrast, majority of pathogenic microorganisms are transported by PW, which carries fourfold more bacteria and 1.5-fold higher fungal genera than SW. Notably, PW transports 1.5-fold higher pathogenic bacterial genera than SW and two-fold higher compared to clouds. Several potential human pathogenic bacterial and fungal genera like Pseudomonas, Acinetobacter, Staphylococcus, Corynebacterium, Aspergillus, Penicillium, Trichosporon, and Phaeococcomyces are dominant in Arctic atmosphere. As many of these genera are commonly associated with respiratory and skin infections, and their presence highlights the need for continued microbial monitoring and research to better understand potential emerging health concerns.