Bacterial typing by Raman spectroscopy is based on small spectral differences that exist between strains, due to differences in their overall molecular composition. These strain-specific spectral differences can be obscured by sources of non-specific signal variance. One such source is the signal contribution of microbial pigments that can vary strongly in intensity. Examples of such pigments are carotenoids in Staphylococcus aureus, and other pigments in Pseudomonas aeruginosa and Mycobacterium lentiflavum. The variance in the intensity of these pigments greatly overshadows strain-specific differences, and therefore lowers spectral reproducibility and causes misclassification of microbial strains. Here a method is presented to determine the spectral signature of pigments of which the relative signal contribution decreases under laser irradiation; so-called photo-bleachable pigments. These signatures are used to eliminate signal variance caused by these pigments by means of the extended multiplicative scatter correction algorithm and spectral interferent subtraction. Application of this method increases the reproducibility of the spectra of microorganisms that contain such pigments to the extent that reproducible identification of samples at strain level is achieved.