A switching voltage converter using an isolated topology includes a transformer for coupling power from an input source to an output load. The transformer must be protected to prevent saturation of its core due to excessive magnetic flux density as the transformer transfers power from its primary side to its secondary side. The magnetic flux is estimated using a voltage measured on the primary or secondary side of the transformer, wherein the secondary-side voltage may be a rectified voltage. If the estimated magnetic flux is detected as approaching a saturation level of the transformer core, any power being input to the transformer is curtailed. This may be accomplished by modifying pulse-width modulated (PWM) waveforms controlling power switches that control the input power transferred to the transformer. Using these techniques, transformer saturation may be avoided without requiring a significantly oversized transformer within the voltage converter.