Understanding microbial migration and survival mechanisms in dust events can elucidate genetic and metabolic exchange between environments and help predict the atmospheric pathways of ecological and health-related microbial stressors. Dust-borne microbial communities have been previously characterized, but the impact of active bacteria within transported communities remains limited. Here, we analyzed samples collected during dust events in Israel, using amplicon sequencing of the 16S rRNA genes and transcripts. Different air trajectories and wind speeds were associated not only with microbial community composition variations but also with those of active bacteria. Active dust-borne bacteria exhibited positive interactions, including highly active carbon and nitrogen cycling bacteria, potential degraders of heavy metals and organic compounds, biofilm-forming, and pathogenic bacteria. This study provides insights into the potential interactive relationships and survival of active microorganisms within the extreme dust environment.