Methods and systems for performing interference mitigation (immunity management) in a radio communication device. A list of frequencies is provided from at least one radio subsystem to an immunity management (IMM) module. The IMM module determines whether any of the frequencies in the list represent a conflict with harmonics associated with one or more clock frequencies associated with one or more embedded systems. If a conflict exists, then the IMM module makes a change in the fundamental frequency of the corresponding clock to remove the conflict, while also ensuring that other frequencies in the list are not impacted by the change. The potential need to change clock frequencies can be evaluated at state transitions of the device, e.g., call establishment, call release, handover or channel re-allocation events.