Apparatuses and methods for operating a modulation system using a flexible reference frequency signal are disclosed. A modulation system uses a phase-locked loop (PLL). An internal reference signal source is configured to provide an internal reference signal having an internal frequency that is substantially independent of the reference frequency. A frequency signal source is configured to provide a plurality of first samples of the frequency signal taken at a first sampling frequency according to the internal reference signal. A resampling device is configured to receive and resample the plurality of first samples to generate a plurality of second samples taken at a second sampling frequency according to the reference frequency. A loop gain compensation device is configured to receive the reference frequency and apply an offset gain to inversely offset a change in PLL loop gain responsive to a change in the reference frequency.