The monitoring of trace metals in microbial cells is relevant for diagnosis of inflammatory bowel disease (IBD). Sulfate-reducing bacteria (SRB) represent an important factor in the IBD development. The content of trace metals in bacterial cells may reflect the functioning of the enzyme systems and the environmental impact on the occurrence of SRB. The aim of our research was to compare the content of trace elements in the cells of SRB cultures isolated from fecal samples of patients with IBD and healthy people. The contents of 11 chemical elements in the bacterial cells of SRB were analyzed by the inductively coupled plasma-mass-spectrometry (ICP-MS) method. Significant changes in the content of calcium, zinc, magnesium, potassium, and iron were observed in patients with IBD compared to healthy individuals. Through a principal component analysis (PCA), a total variability of 67.3% in the difference between the samples was explained. The main factors influencing the total variability in the bacterial cells of SRB isolated from patients suffering from IBD were the content of the micro- and trace elements, such as manganese (with power 0.87), magnesium and cobalt (0.86), calcium (0.84), molybdenum (0.81), and iron (0.78). Such changes in the elemental composition of SRB under different conditions of existence in the host may indicate adaptive responses of the microorganisms, including the inclusion of oxidative stress systems, which can lead to changes in SRB metabolism and the manifestation of parameters of IBD in humans. The use of PCA might make it possible in the future to predict the development and ratio of SRB in patients with various diseases.