A multifunctional infrared spectrometer system has an interferometer which receives the infrared beam from a source and provides a modulated output beam on beam paths to multiple spatially separated infrared detectors. A multi-position mirror element mounted at a junction position receives the beam on a main beam path and directs it on branch beam paths to sample positions, with the beam then being directed on the branch beam path to one of the detectors. One of the branch beam paths may include a sample holder at the sample position which can index between a position at which a sample is analyzed, to a reference material position, to a pass-through position for calibration purposes. The multi-position mirror element may also be indexed to direct the beam on a branch path to a fiber optic cable which has a probe at the end of it which may be inserted in a sample fluid or powder to be analyzed, with the reflected light from the probe being directed back on an optical fiber cable to a detector at the spectrometer. The multi-position mirror element may be moved to a position at which the beam is directed on a beam path to and through an integrating sphere to a solid sample, with the reflected light from the sample being directed by the surfaces of the integrating sphere to a detector. A detector may be mounted to detect the light transmitted through the sample to obtain measurements of both reflected and transmitted infrared light at the sample.