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CAN required CLK_CANx_APB and CLK_CANx_APB to be running and will not request any clock by itself. We can ensure both clocks to be running by preventing the MCU from entering IDLE state. The SAMD5x/SAME5x Family Data Sheet says in Section "39.6.9 Sleep Mode Operation" says: > The CAN can be configured to operate in any idle sleep mode. The CAN > cannot operate in Standby sleep mode. > > [...] > > To leave low power mode, CLK_CANx_APB and GCLK_CANx must be active > before writing CCCR.CSR to '0'. The CAN will acknowledge this by > resetting CCCR.CSA = 0. Afterwards, the application can restart CAN > communication by resetting bit CCCR.INIT. tl;dr: At most SAM0_PM_IDLE is allowed while not shutting down the CAN controller, but even that will pause communication (including RX). Apparently, the CAN controller was never tested without also using the USB peripheral, which kept the clocks running as side effect.