A microwave processing system includes: a broadband variable frequency microwave (VFM) source; a plurality of waveguide applicators, each of which includes a waveguide transition and is capable of supporting a selected subset of frequencies within the bandwidth of the broadband VFM source; a microwave switching means allowing the microwave source to be connected to any one of the waveguide transitions so that microwave power is delivered to the corresponding waveguide applicator; and wherein each of the waveguide applicators includes at least one channel through which a microwave transparent tube may be run so that process fluid flowing through the tube may be exposed to microwave power in the applicator. A related method is also disclosed.