Electronic devices such as portable electronic devices contain electronic components. The electronic components may include radio-frequency transceiver circuitry. The radio-frequency transceiver circuitry may be used for handling data communications and cellular telephone voice communications. One or more adjustable clock sources may be provided within the electronic device. The adjustable clock sources may be based on phase-locked-loop circuits. A clock manager may determine which frequencies are being used by the radio-frequency transceiver circuitry and other components in the electronic device. The clock manager may use this information to compute a list of safe fundamental clock signal frequencies. Based on the list of safe clock signal frequencies, the clock manager may dynamically adjust the clock sources to avoid collisions between harmonics of the clock signals from the clock sources and the frequencies used by the transceiver circuitry and other components.