Yeastolate or yeast extract, which are hydrolysates produced by autolysis of yeast, are often employed as a raw material in the media used for industrial mammalian cell culture. The source and quality of yeastolate can significantly affect cell growth and production; however, analysis of these complex biologically derived materials is not straightforward. The best current method, liquid chromatography–mass spectrometry (LC‐MS), is time‐consuming and requires extensive expertise. This study describes the use of surface‐enhanced Raman scattering (SERS) and fluorescence excitation–emission matrix (EEM) spectroscopy coupled with robust principal component analysis (ROBPCA) for the rapid and facile characterization and discrimination of yeast extracts in aqueous solution. SERS using silver colloids generates time‐dependent signals, where adenine is the strongest contributor, and the spectra are stable and reproducible (< ~3%) at 180 min after mixing. Combining this spectral behavior with chemometric methods enables SERS to be used in discriminating between different yeastolate sources, for assessing lot‐to‐lot variability, and, potentially, to monitor storage‐induced compositional changes. Fluorescence EEM combined with multiway ROBPCA also provides a rapid and inexpensive method for the discrimination of yeastolate, yielding results in terms of sample discrimination very similar to that obtained with SERS. However, the EEM data does not provide the same level of chemical information that is provided by the SERS. Thus, the combination of these two methodologies has the potential to be extremely useful in biopharmaceutical manufacturing, as well as for the rapid characterization and screening of biogenic hydrolysates from animal or plant sources. Copyright © 2011 John Wiley & Sons, Ltd.