The method of microbiological decontamination of a machine comprising an enclosure (5, 100) for treating a support (6) and a conveyor comprising a shuttle (30), comprises the steps of obtaining a container (6) adapted to be received on said shuttle (30) and to diffuse biocidal agent in said enclosure (5, 100), of placing said container (6) on said shuttle (30), of moving said shuttle (30) within said enclosure, and of evacuating said agent. The microbiological analysis system comprises a container (6), a microbiological analysis machine comprising at least two stations (2, 3, 4) for treatment of said support (6), a conveyor comprising a shuttle (30) adapted to receive and to move said support (6), said container (6) being adapted to be received on said shuttle (30), as well as means (150, 156, 159) for evacuating said biocidal agent.