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The atmosphere plays an important role in transporting microorganisms on a global scale, yet the processes affecting the composition of the airborne microbiome, the aerobiome, are not fully outlined. Here we present the community compositions of bacteria and fungi obtained by DNA amplicon-sequencing of aerosol samples collected in a size-resolved manner during nine consecutive days in central Israel. The campaign captured dust events originating from the Sahara and the Arabian deserts, as well as days without dust (“clear days”). We found that the source of the aerosol was the main variable contributing to the composition of both fungal and bacterial communities. Significant differences were also observed between communities representing particles of different sizes. We show evidence for the significant transport of bacteria as cell-aggregates and/or via bacterial attachment to particles during dust events. Our findings further point to the mixing of local and transported bacterial communities, observed mostly in particles smaller than 0.6 μm in diameter, representing bacterial single cells. Fungal communities showed the highest dependence on the source of the aerosols, along with significant daily variability, and without significant mixing between sources, possibly due to their larger aerodynamic size and shorter atmospheric residence times. These results, obtained under highly varied atmospheric conditions, provide significant assurances to previously raised hypotheses and could set the course for future studies on aerobiome composition.