Non-invasive flesh firmness prediction using near infrared spectroscopy has been perfected and validated on three apple varieties. Three novel calibration models were developed following three year's of repeated large-scale sampling of stored commercial apple varieties ‘Gala’, ‘Red Jonaprince’ and ‘Jonagored’. The spectroscopic results were compared directly with those obtained using the invasive method. Increased accuracy of calibration models was achieved with the newly established data collection model. The results exhibited coefficient of determination for calibration, R2, and ratio of prediction to deviation (RPD) in excess of 0.91 and 2.3, respectively, thus enabling excellent prediction of flesh firmness via a non-invasive and fast spectroscopic approach. The highest R2 obtained was 0.94, RPD 2.6 root mean square error of calibration 5.87 N, and root mean square error of cross-validation (internal) 6.75 N were found for variety ‘Red Jonaprince’. Our complex long-term study provided excellent external validated calibration models and the approach can help developing calibration models for commercial sorting lines using near infrared spectroscopy.