The electronic structure of individual sheets of the bacterial surface protein layer (S layer) of Bacillus sphaericus NCTC 9602 was studied using a photoemission electron microscope (PEEM) operating in near-edge X-ray absorption fine structure spectroscopy mode. The laterally resolved measurements performed at the C 1s, N 1s, and O 1s thresholds on fresh samples revealed characteristic differences compared to the laterally integrated data, where substrate contributions were taken along with the protein signals. During the PEEM experiments an irradiation-induced increase of the C-C bond density at the cost of the densities of the C-O and C-N bonds related to a rearrangement of the contributing atoms of the S layer deposited onto a Si substrate was observed. The critical irradiation doses for the C-O and C-N bond breaking and formation of the new C-C bonds were derived.