A new methodology is proposed to describe the evolution of the main chemical compounds of grape must during wine alcoholic fermentation using Attenuated Total Reflectance Mid Infrared (ATR-MIR) spectra in combination with Multivariate Curve Resolution Alternating Least-Squares (MCR-ALS). In addition, we have developed a process control strategy to detect differences between fermentations running under Normal Operation Conditions (NOC) and fermentations intentionally spoiled with lactic acid bacteria at the beginning of alcoholic fermentation (MLF) to promote deviations from NOC. MCR-ALS models on these data showed a good data fit (R2 = 99.95% and lack of fit = 2.31%). It was possible to resolve the spectral profiles of relevant molecules involved in the alcoholic fermentation process, including the one related to bacterial spoilage (lactic acid). MSPC charts were built based on the concentration profiles obtained from the MCR-ALS models and using T2 and Q statistics. Spoiled wines showed off-limit values for T2 after 96 h, making it possible to detect lactic acid bacteria spoilage in early stages of alcoholic fermentation. Thus, the use of ATR-MIR spectra and MCR-ALS analysis shows a great potential for a rapid control of the state of the alcoholic fermentation process, making it possible to early detect the appearance of undesired molecules during the process, which allows the winemaker to apply corrective measures and obtain a good final product.