Refrigerant management control is provided for an air conditioning system (10) with cool thermal energy storage. The system includes a compressor (18), a condensing unit (12), a temporary refrigerant storage vessel (28), a storage module (14) containing a thermal energy storage medium (35), a liquid refrigerant pump (42) associated with the storage module, expansion means (62) and an evaporator (16) operatively interconnected. The system is operable in a shift cooling mode, direct cooling mode, and storage medium cooling mode. Before the system is operable in the shift cooling mode, the system is operated in a first transitory mode wherein the storage module (14) is utilized as a heat sink to draw refrigerant from the condensing unit (12), temporary refrigerant storage vessel (28) and evaporator (16) into the storage module (14). Before the system is operable in the direct cooling mode, the system is operated in a second transitory mode wherein the compressor (18) is operated to draw refrigerant into the condensing unit (12) and temporary refrigerant storage vessel.