In the oligotrophic waters of the Mediterranean Sea, during the stratification period, the microbial loop relies on pulsed inputs of nutrients through the atmospheric deposition of aerosols from both natural (e.g., Saharan dust), anthropogenic, or mixed 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 environmental conditions (+3 ^∘C warming and acidification of −0.3 pH units), through experiments in 300 L climate reactors. In total, three Saharan 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 (ProcEss studies at the Air-sEa Interface after dust deposition in the MEditerranean sea) 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 d experiments. Different microbial and viral responses to dust were observed rapidly after addition and were, most of the time, more pronounced when combined with future environmental conditions. The dust input of nutrients and trace metals changed the microbial ecosystem from a bottom-up limited to a top-down controlled bacterial community, likely from grazing and induced lysogeny. The relative abundance of mixotrophic microeukaryotes and phototrophic prokaryotes also increased. 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.