Presented are joint active thermal management (JATM) systems with heat exchanger storage of surplus refrigerant, methods for making/operating such systems, and vehicles equipped with such systems. A JATM system includes a coolant loop that fluidly connects to a vehicle battery system for pumping thereto coolant, an oil loop thermally coupled to the coolant loop and fluidly connected to a vehicle powertrain system for pumping thereto oil, and a refrigerant loop thermally coupled to the coolant loop and operable to circulate refrigerant for heating/cooling a passenger compartment. An electronic controller determines if a current amount of refrigerant in the refrigerant loop exceeds a calibrated threshold for the current operating mode of the JATM system. If so, the controller determines if one of the refrigerant loop's heat exchangers is available to store excess refrigerant. If the heat exchanger is available, the refrigerant loop stores excess refrigerant in the available refrigerant heat exchanger.