In the oligotrophic waters of the Mediterranean Sea, during the stratification period, the microbial loop relies on pulsed inputs of nutrients through atmospheric deposition of aerosols from both natural (Saharan dust) and anthropogenic origins. While the influence of dust deposition on microbial processes and community composition is still not fully constrained, the extent to which future environmental conditions will affect dust inputs and the microbial response is not known. The impact of atmospheric wet dust deposition was studied both under present and future (warming and acidification) environmental conditions through experiments in 300 L climate reactors. Three dust addition experiments were performed with surface seawater collected from the Tyrrhenian Sea, Ionian Sea and Algerian basin in the Western Mediterranean Sea during the PEACETIME cruise in May–June 2017. Top-down controls on bacteria, viral processes and community, as well as microbial community structure (16S and 18S rDNA amplicon sequencing) were followed over the 3–4 days experiments. Different microbial and viral responses to dust were observed rapidly after addition and were most of the time higher when combined to future environmental conditions. The input of nutrients and trace metals changed the microbial ecosystem from bottom-up limited to a top-down controlled bacterial community, likely from grazing and induced lysogeny. The composition of mixotrophic microeukaryotes and phototrophic prokaryotes was also altered. Overall, these results suggest that the effect of dust deposition on the microbial loop is dependent on the initial microbial assemblage and metabolic state of the tested water, and that predicted warming, and acidification will intensify these responses, affecting food web processes and biogeochemical cycles.