The objectives of this study were (i) to test different conditions of freezing, thawing, and grinding during sample preparation and (ii) to evaluate the possibility of using mid-infrared spectroscopy for analyzing the composition of sugars, organic acids, and polyphenols in apples. Seven commercial apple cultivars were chosen for their large variability in composition (total polyphenols from 406 to 1033 mg kg −1 fresh weight). The different conditions of sample preparation affected only the phenolic compounds and not sugars or organic acids. The regression models of the mid-infrared spectra showed a good ability to estimate sugar and organic acid contents (R 2 ≥ 0.96), except for citric acid. Good predictions were obtained for total phenolic, flavan-3-ols, and procyanidins (R 2 ≥ 0.94) provided oxidation was avoided during sample preparation. A rapid and simple procedure was then proposed for phenolic compounds using sodium fluoride during sample homogenization at ambient temperature and freeze-drying before spectra acquisition. Mid-infrared (MIR) has been shown to be a suitable technique for high-throughput analysis of the major constituents in fruit juices, homogenates, and extracts. 1−7 These studies have been aimed to assay soluble solids content, titratable acidity, and the concentrations of individual sugars, organic acids, and total phenolic compounds. It would be highly beneficial if it could also be applied to the analysis of specific metabolites such as individual polyphenols. Indeed, the quantification of these compounds requires chemicals and solvents, equipment such as high-performance liquid chromatography coupled to a diode array detector, good technical skill, and time. However, the development of high-throughput analyses has been hindered by the high reactivity of some molecules such as polyphenols. Hence, this study aimed at identifying the simplest and cheapest sample preparation for MIR application for poly-phenol quantification. The fruit chosen for this methodological optimization was apple, as it is among the most consumed fruits worldwide and indeed a good source of polyphenols in the French diet. 8 A regular consumption of apples provides a large amount of polyphenolic compounds such as flavan-3-ols (procyanidins and catechins), dihydrochalcones (phloridzin), hydroxycinnamic acids (chlorogenic acid and p-coumaroyl-quinic acid), flavonols (quercetin), and anthocyanins. A large variability exists according to the studied cultivars with, for example, a variation of total phenolic content between 523 and 2724 mg kg −1 dry weight (DW) among 67 new and old apple varieties. 9