A control methodology for a two-stage PWM DC-DC conversion system, with transformer-isolation, in which the converter circuit input voltage is compared to a set voltage calibrated as a function of the desired output voltage and the maximum voltage conversion ratio provided by the second-stage converter. When the input voltage is above the set voltage, the second-stage converter is controlled to provide both output voltage regulation during normal operation and output current limiting during over-current conditions. However, when the input voltage is below the set voltage, the first-stage converter is controlled to provide output voltage regulation with minor output current limiting, and the second-stage converter is controlled to provide extended output current limiting independent of the input voltage.