In this chapter, a step-by-step protocol is presented regarding the application of Fourier transform infrared spectroscopy (FT-IR) for monitoring changes in saffron apocarotenoids upon storage. Saffron (Crocus sativus L.) is the most expensive spice in the market worldwide. So far, the apocarotenoid content of the dried plant flower stigmas that constitute saffron is assessed spectrophotometrically in aqueous extracts and expressed as coloring strength values according to international trade standard procedures and specifications (ISO, Codex Alimentarius). This quality parameter serves as one of the key criteria that help to distinguish the commercial categories of the traded product. The workflow that is described herein enables an insightful in situ investigation of biochemical changes that may take place during the storage of freshly produced saffron through FT-IR spectra monitoring. The protocol assesses instrumental options with different sampling modes available and details standard procedures for reproducible sample preparation and spectral data acquisition. A sequence of steps including the preprocessing, quality control, and biochemical assignment of the data is explained. Above all, the spectral features of diagnostic importance for apocarotenoid loss and quality deterioration are highlighted to facilitate future applications of FT-IR spectroscopy to the quality control of this valuable product.