See [this line in SPI.cpp](https://github.com/arduino/ArduinoCore-renesas/blob/149f78b6490ccbafeb420f68919c381a5bdb6e21/libraries/SPI/SPI.cpp#L386C38-L386C38) `spcmd0 &= !(((uint32_t)0xFF) << 2);` should be `spcmd0 &= ~(((uint32_t)0xFF) << 2);` The logical not makes the mask 0 and wipes out the earlier settings. Should be a bitwise not to make the mask FFFFFC03.