Magnetic resonance imaging (MRI) is considered being state-of-the-art technology for body composition analysis. Compared to other indirect techniques such as scales, calipers, bioimpedance, and dual-energy X-ray absorptiometry (DXA), MRI offers direct and precise measurements of the volumes of different tissue compartments and also enables quantification of diffuse fat infiltration in organs. Here, we describe a protocol for acquiring of fat–water-separated MRI data and the image postprocessing required for the quantification of several body composition biomarkers relevant for metabolic research. This protocol has successfully been used in several clinical studies and also in the large UK Biobank population study.