The use of Fourier Transform Infrared Spectroscopy (FTIR) coupled to multivariate analysis made possible to monitor the degradation of bioactive compounds during the drying process of red pepper in a tray dryer. The FTIR spectra were obtained at different drying times and temperatures and showed variation among them. This behavior provided the possibility of assessing the degradation of functional compounds present in red pepper along the drying process by a chemometric model. The chemometric model obtained, correlated the quality parameters considered at different drying times and the corresponding FTIR spectra, and was developed with the PLS algorithm, which showed the best correlation between the bioactive compounds and the spectral images, obtaining R² values greater than 0.99 for all properties analyzed. Critical regions during the drying process were identified where change in the operating conditions could be performed to preserve the product quality. Drying times larger than those required to give final product moisture of 0.1 d.b. caused severe degradation in all analyzed parameters (carotenoids, ascorbic acid, total phenols and antioxidant activity).