Recently, Raman spectroscopy has become more and more into the focus of bacterial identification as it is a culture-independent, non-destructive and contact-less method. Since Raman spectroscopy is a phenotypic method lots of parameters can influence the spectra. One of the least controllable factors is transport and storage but it is often not taken into account and therefore these influences on the Raman spectra of bacteria are unknown. In order to investigate this effect, we simulated the transport and storage of bacteria under different conditions and investigated them with Raman spectroscopy. With a look at the mean spectra, only one bacterium showed differences during the storage conditions. However, after applying chemometric methods, changes in the data could be found within all bacteria during storage times. This study shows how drastic the effect will influence a database, depending on the different handling or storage. Therefore, it is of utmost importance to consider these non-biological influences when planning further experiments and evaluating the resulting data.