Different spectroscopic techniques based on infrared and Raman were used to evaluate the natural wax and related surface quality of apple fruit. Transmission near-infrared (NIR) spectroscopy was applied to solutions of single wax components and extracted apple wax. Fourier transform infrared (FTIR) spectroscopy was used for transmission measurements of wax films on NaCl crystals, diffuse reflectance spectroscopy (DRIFTS) was used to analyze wax powders, and FT-Raman spectroscopy was explored to examine intact wax layers on whole fruit. The natural wax layers of apple fruit from a maximum of three different cultivars (Jonagold, Jonagored, and Elshof) from three picking dates (early, commercial, and late), three controlled atmosphere storage durations (0, 4, and 8 months), and three shelf life periods (0, 1, and 2 weeks) within each storage duration were examined. Canonical discriminant analysis was carried out on the first derivative NIR and FTIR spectra to describe the information contained in the spectra. Discrimination between cultivars and between storage duration based on wax layer properties was achieved with reasonable accuracy from both of the techniques. Information contained in the spectra of apples from different picking dates and shelf life periods was not significant. Differences between cultivars and storage periods in this analysis mostly related to differences in the number of aliphatic chains (e.g., alkanes and esters) and the presence of alpha-farnesene. No satisfactory results were obtained by means of Raman spectroscopy and DRIFTS.