Molecularly imprinted polymers (MIPs) are artificial recognition materials mimicking biological recognition entities such as antibodies. The general model of imprinting assumes that functional monomers interact with functional groups present on the target species which leads to cavities complementing the template in surface chemistry and shape thus ensuring recognition. However, to date there is little independent experimental evidence supporting that the surface chemistry in the imprints is tailored to analyte recognition and thus differs from the surface chemistry of the surrounding polymer. Herein, we investigate such chemical differences between imprints of Escherichia coli and Bacillus cereus in poly(styrene-co-DVB) and a commercial acrylate-based polymer by the means of confocal Raman microscopy and PLS-DA. The MIPs were generated using a stamping approach. Peak-force QNM measurements were conducted to rule out residues of bacterial cells in the imprints. While imprints of E. coli and B. cereus could be distinguished based on their Raman spectra in the acrylate-based polymer, differentiation in poly(styrene-co-DVB) was not significant. This could be a result of a higher potential of acrylate functional groups for interacting with lipopolysaccharides and peptidoglycans on bacteria surfaces compared to the phenyl groups of poly(styrene-co-DVB) and emphasizes the importance of the right choice of functional monomers for a specific target analyte.