This chapter details the protocols for analysis of citrus by-products by using FTIR via sample preparation, spectral acquisition, and data interpretation. This includes steps that are essential for enabling the process, such as baseline correction, peak identification, and quantification of functional groups, in a manner that conforms to calibration curves and the Beer–Lambert law. Peak intensity and area calculations are discussed, along with approaches to mitigate the most common challenges (sample interference and atmospheric water vapor); key precautions and best practices, such as sample preparation, instrumentation calibration, and minimizing contamination for reliable results, are discussed.