Near-infrared spectroscopy (NIRS) is often criticized due to its insufficient accuracy in determining body composition compared to the gold standard methods. In this work, we show that the use of multiple source-detector distances, as well as the simultaneous use of physiological and optical features, can significantly improve the accuracy of determination of fat and lean mass percentage in the human body using NIR spectroscopy. The study performed on the n = 292 cohort revealed the mean absolute errors of 3.5% for fat content and 3.3% for soft lean mass percentage prediction (r = 0.93) using the multifrequency bioimpedance analysis (BIA) as a reference. Hence, NIRS can serve as an independent reliable method for body composition analysis with precision close to that of advanced multifrequency BIA.