Industrially tempered dark chocolate processed under different conditions was analyzed using Attenuated Total Reflection-Fourier Transform-Infrared spectroscopy (ATR-FT-IR). Spectra were collected during the cooling process right after tempering using two distinct machines and machine operational modes and over short and long storage (1 day and two months, respectively). To interpret the spectra collected, Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) analysis was used. MCR-ALS incorporated a dedicated implementation of hard modeling constraints for the elucidation of the spectral and concentration profiles of chocolate contributions during the monitored process with the aim of reducing ambiguity in the data interpretation. Thus, the spectral signature of the amorphous form of chocolate was constrained to follow a Gaussian shape, in line with previously reported works and with measurements observed at the beginning of the cooling process. Additionally, hard modeling constraints were applied to the concentration profiles linked to the cooling process by implementing the Avrami kinetic model, often postulated to describe thermally induced fat crystal transformations. The application of the hard modeling constraints eased the generation of interpretable solutions and resulted in concentration profiles and spectral signatures that were defining much better the crystal state of the chocolate samples. A two-component system explained the studied procedures, with a contribution S₁ representing the highly crystalline state of the chocolate fats and S₂ representative of the amorphous/less stable state. In general, we were able to track the transition from a less ordered to a highly ordered crystal state of the fats during the cooling stage of chocolate. After short storage, the chocolates had contributions of both S₁ and S₂ profiles. After long storage, the S₁ crystalline form was the most dominant interpreted as the reorganization of the triglyceride acyl chains towards a thermodynamically favorable state. The latter was observed for all analyzed chocolates, implying that, regardless the tempering process or temper regime tested, the fats in chocolates reach the same high crystalline state after maturing.