The control of virgin olive oil (VOO) freshness requires new tools that reflect the diverse chemical changes that take place during the market period. Fluorescence spectroscopy is one of the techniques that has been suggested for controlling virgin olive oil (VOO) freshness during its shelf-life. However, a complete interpretation of fluorescence spectra requires analyzing multiple parameters (chemical, physical–chemical, and sensory) to evaluate the pace of fluorescence spectral changes under moderate conditions with respect to other changes impacting on VOO quality. In this work, four VOOs were analyzed every month with excitation–emission fluorescence spectra. The same samples were characterized with the concentration of fluorophores (phenols, tocopherols, chlorophyll pigments), physical–chemical parameters (peroxide value, K232, K270, free acidity), and sensory attributes (medians of defects and of the fruity attribute). From the six components extracted with parallel factor analysis (PARAFAC), two components were assigned to chlorophyll pigments and those assigned to tocopherols, phenols, and oxidation products were selected for their ability to discriminate between fresh and aged oils. Thus, the component assigned to oxidation products correlated with K270 in the range 0.80–0.93, while the component assigned to tocopherols–phenols correlated with the fruity attribute in the range 0.52–0.90. The sensory analysis of the samples revealed that the changes of these PARAFAC components occurred at the same time as, or even before, the changes of the sensory characteristics.