Changes in chemical and quality characteristics of olive oils were evaluated with respect to pre and post-harvest factors such as: olive type, harvest time, malaxation temperature, and storage at room temperature. Additionally, discriminative and predictive capacities of UV-vis, near infrared (NIR), mid infrared (MIR) spectra and electronic nose data on olive oils by using multivariate statistical tools were studied. Varietal and harvest time differences were the most significant factors influencing the quality and chemical properties of Ayvalik and Memecik olive oils. Malaxation temperature was significant on a number of phenolic compounds such as tyrosol, hydroxytyrosol and pinoresinol, and peroxide value. Olive oils of early and mid-harvest were higher in phenolic alcohols, and pigments content, whereas peroxide values, linoleic and stearic acids characterized late harvest oils. Storage for 15 months at room temperature in dark facilitated evolution of some important phenols, while increasing the content of ethyl and methyl esters at varying degrees among varieties. There were no significant changes in fatty acids and acidity contents of the oils. However, total phenol content and oxidative stability declined and a significant depletion of colors and pigments contents occurred. Multivariate regression analysis indicated that lipid-based variables are the most consistent contributors (positive or negative) to olive oil oxidative stability. UV-vis, MIR, NIR spectroscopies and e-nose data were excellent varietal and harvest season discriminating tools. Pigments were well predicted by UV-vis, while MIR performs better in the prediction of fatty acids, alkyl esters, oxidative stability and free fatty acid.