Mineral dust is an air pollutant that has been linked to respiratory and cardiovascular diseases. During the Harmattan annual season, large regions in Western Africa, including the islands of Cape Verde, are exposed to high concentrations of mineral dust that gets emitted from areas in the Sahara and transported over long distances. Both the chemical composition and the microbiological properties of dust may influence its detrimental health impact, but their specific effects have rarely been disentangled. We investigated the microbiome associated with aerosol particles collected at the Cape Verde island Sao Vicente, comparing reference periods with low dust concentrations to periods with pronounced Saharan dust storm events. Samples were collected simultaneously on the island's east coast where the dust arrived ('inflow' site) and on the northwest coast close to the island's major city ('outflow' site). By doing so, we wanted to elucidate which microorganisms had been transported with the dust from the African continent and which had originated from the island itself. 16S rDNA amplicon sequencing revealed that Saharan dust carried enormous microbial diversity. The most abundant bacterial taxa were also represented among strains successfully cultivated. The microbial composition of collected aerosols changed between dust storm events and reference periods, but also between in- and outflow sites on the island. Dust events were characterized by increased relative abundances of the genera Domibacillus sp., Acinetobacter sp. and Cytophaga sp. which contain several opportunistic pathogens. Further analysis showed that samples taken at the outflow site contained higher relative abundances of Nocardioides sp., Acinetobacter sp. and Pseudomonas sp., which presumably had been mobilized from sources on the island. Inflow samples were distinguished by lower relative abundances of certain bacteria. This may be caused by the large continental area from which the dust had been mobilized, resulting in a diverse microbiome with few dominating organisms. Lastly, the method of sampling clearly had an effect on the observed results, which should be considered in future studies.