The production of chocolate treats with a long shelf-life and desirable organoleptic characteristics depends, at a first stage, on proper tempering and cooling during manufacturing. These process steps control the formation and the structure of the fat crystal network, which should predominately consist of triacylglycerols (TAGs) in the β (V) polymorphic form. This study uses Fourier Transform-Infrared spectroscopy by Attenuated Total Reflection (ATR-FT-IR) to examine the formation of the fat crystal structure in cocoa butter and dark chocolate during cooling under laboratory conditions. ATR-FT-IR was also used to analyse chocolates that were produced by industrial scale equipment, tempered at different processing settings. Spectra acquired during cooling and storage were processed by Multivariate Curve Resolution (MCR). MCR provides quantitative and qualitative information on the dominant polymorphs in the chocolate samples, expressing structural information of the TAGs (glycerol conformation, sub-cell packing, chain configuration, etc.). Using this combination of analytical methods and data modelling, it was possible to identify chocolates with increased conformational regularity of the hydrocarbon chains and differentiate samples that had a mixed profile of ordered and disordered chain configurations.