Pin configuration is missing PIN_ATTR_TIMER, in order to get PWM working on the channel { PORTA, 17, PIO_PWM, (PIN_ATTR_DIGITAL|PIN_ATTR_PWM|PIN_ATTR_TIMER), No_ADC_Channel, PWM2_CH1, TCC2_CH1, EXTERNAL_INT_1 }, // TCC2/WO[1] Above is copied from arduino_zero variant.