A method for operating a LED lighting system at a target output color is provided. The LED system includes a color sensor and three or more LED emitters each operable at a controllable emitter drive setting. The method provides at least one calibration matrix defining a relationship between measurements obtained from the color sensor, represented by sensor color point coordinates, and absolute color point coordinates in an absolute color space. In some embodiments, a calibration matrix defining a non-linear relationship between the two color spaces is provided. In other embodiments, individual calibration matrices are provided for each LED emitter.