In food industry, safety and quality are considered important issues worldwide that are directly related to health and social progress. Meat spoilage is the result of decomposition and the formation of metabolites, caused by the growth and enzymatic activity of microorganisms, and it presents not only a health hazard but an economic burden to the producer. In this research work, we explore the potential of Fourier transform infrared (FTIR) spectroscopy in combination of principal components analysis and neuro-fuzzy modelling, to determine beef spoilage microorganisms during aerobic storage at chill and abuse temperatures. FTIR spectra were obtained from the surface of beef samples, while culture microbiological analysis determined the total viable count (TVC) for each sample. The dual purpose of the proposed modelling approach is not only to classify beef samples in the respective quality class (i.e., fresh, semi-fresh and spoiled), but also to predict their associated microbiological population directly from FTIR spectra. The proposed neuro-fuzzy network model utilises a prototype defuzzification scheme, whereas the number of input membership functions is directly associated to the number of rules, reducing thus, the “curse of dimensionality” problem. Results confirmed the superiority of the adopted methodology compared to other schemes such as multilayer perceptron and the partial least squares techniques and indicated that FTIR spectral information in combination with an efficient choice of a learning-based modelling scheme could be considered as an alternative methodology for the accurate evaluation of meat spoilage.