An information handling system includes a processor, a system baseboard management controller (BMC), and a field-programmable gate array (FPGA) add-in card. The FPGA add-in card includes an FPGA programmed with accelerated function units (AFUs) to perform processing tasks for the processor. The AFUs include AFUs of a common type. A card BMC provides a temperature indication to the system BMC. The system BMC determines that a temperature of the FPGA add-in card exceeds a temperature threshold based upon the temperature indication, selects one of the common AFUs to be disabled, and directs the card BMC to disable the selected AFU. The card BMC disables the first AFU and not the second AFU in response to the direction to disable the first AFU.