A Built-in Self Test (BIST) system is provided in a Field Programmable Gate Array (FPGA) that can adjust test signal patterns provided for testing after partial reconfiguration of the FPGA. The BIST system includes a decoder that monitors I/O signals and provides an output indicating when I/O signals change indicating partial reconfiguration has occurred. The decoder output is provided to a BIST test signal generator providing signals to an IP core of the FPGA as well as a BIST comparator for monitoring test results to change test signals depending on the partial configuration mode.