Infrared spectroscopy (wavelengths ranging from 750–25,000 nm) offers a rapid means of assessing the chemical composition of a wide range of sample types, both for qualitative and quantitative analyses. Its use in the food industry has increased significantly over the past five decades and it is now an accepted analytical technique for the routine analysis of certain analytes. Furthermore, it is commonly used for routine screening and quality control purposes in numerous industry settings, albeit not typically for the analysis of bioactive compounds. Using the Scopus database, a systematic search of literature of the five years between 2016 and 2020 identified 45 studies using near-infrared and 17 studies using mid-infrared spectroscopy for the quantification of bioactive compounds in food products. The most common bioactive compounds assessed were polyphenols, anthocyanins, carotenoids and ascorbic acid. Numerous factors affect the accuracy of the developed model, including the analyte class and concentration, matrix type, instrument geometry, wavelength selection and spectral processing/pre-processing methods. Additionally, only a few studies were validated on independently sourced samples. Nevertheless, the results demonstrate some promise of infrared spectroscopy for the rapid estimation of a wide range of bioactive compounds in food matrices.