A refrigerant recovery system that includes a plurality of refrigerant storage containers, each having a refrigerant inlet port and facility for indicating quantity of refrigerant in the container. A refrigerant recovery unit for withdrawing refrigerant from equipment under service includes an outlet port and internal control for enabling operation of the refrigerant recovery unit to provide a flow of recovered refrigerant at the outlet port withdrawn from the equipment under service. A refrigerant flow control manifold connects the refrigerant recovery unit to the plurality of storage containers. The flow control manifold includes control electronics responsive to indication of refrigerant quantity in the several containers for automatically connecting the outlet port of the recovery unit to each of the plurality of containers as quantity of refrigerant in each container in turn reaches a preselected level. The manifold control is also coupled to the control circuitry of the refrigerant recovery unit, and is responsive to quantity of refrigerant in the several storage containers, for preventing operation of the refrigerant recovery unit when all of the containers are full.