The present invention relates to a light emitting diode (LED) lighting system (10) comprising a plurality of LED light sources for generating a mixed color light, the plurality of LED light sources including at least one LED light source comprising at least one LED adapted to emit light of a first wavelength and a wavelength converter for converting at least a portion of the light emitted from the LED(s) to light of another wavelength, and a control system (33) for individually controlling the flux output of the LED light sources. The control system in turn comprises means for providing feedback of the flux of at least one of the LED light sources, the feedback being based on input from an unfiltered sensor (22) responsive to the actual flux of the individual LED light source, for allowing control of the at least one LED light source in accordance with the feedback, and means for providing first control data based on input from a filtered sensor (36) responsive to the first wavelength flux, for allowing adjustment of at least one LED light source, to compensate for first wavelength leakage of the wavelength converted LED light source(s). The present invention also relates to a system and method for controlling a LED lighting unit.