The present invention relates to a method of fully charging an electrical energy storage device using a lower voltage fuel cell system. A fuel cell system includes a fuel cell stack and an EESD electrically coupled to a common high voltage bus line. The EESD has a higher voltage output than the fuel cell stack, and thus the stack is unable to fully charge the EESD, for example, at system shut-down. In order to allow the fuel cell stack to fully charge the EESD, the EESD is separated into a plurality of separate electrical storage banks having lower voltage potentials. A series of contactors are provided to electrically couple the storage banks in series during normal system operation, and separately charge the storage banks using the fuel cell stack so that they are fully charged. The series of contactors can also be configured so that the storage banks can be electrically coupled in series during normal operation of the system and be electrically coupled in parallel during charging at system shut-down.