Abstract: A fuel cell system including a hydrocarbon fuel stream including a sulfur compound; a passive sorbent bed including a selective sulfur sorbent configured to remove the sulfur compound from the hydrocarbon fuel stream; a SCSO reactor, and an active sorbent bed comprising a sulfur oxide sorbent, wherein the active sorbet bed is configured to receive an effluent stream from the SCSO reactor and remove at least a portion of the sulfur oxides via the sulfur oxide sorbent. During start-up of the fuel cell system, the hydrocarbon fuel stream may be directed along a first flow pathway through the passive sorbent bed to remove the sulfur compound from the fuel stream during a first time period and then directed along a second flow pathway during a second time period that does not pass through the passive sorbent bed, e.g., once the SCSO reactor/active sorbent bed have reached operating temperature.