A method and system for automated remote microbial air sampling includes a sampling enclosure positioned outside an isolator. An infeed sample receiver passes sample containers into the enclosure. An atrium is located within the enclosure and exposes containers to a gas sample. A remote sampling device collects the gas sample from the isolator and passes it to the atrium. A load arm is located within the enclosure. The load arm intermittently permits containers to enter the enclosure and moves containers to the atrium. An outfeed sample receiver passes containers out of the enclosure. The system allows addition and removal of containers from the air sampling system without interrupting the processing of the containers within the enclosure, and allows the first container supplied to the air sampling system to be the first exposed container removed therefrom.