In the last decade, an increasingly common method of maize stover management is to use it for energy generation, including anaerobic digestion for biogas production. Therefore, the aim of this study was to provide a chemical and structural characterization of maize stover fractions and, based on these parameters, to evaluate the potential application of these fractions, including forbiogas production. In the study, maize stover fractions, including cobs, husks, leaves and stalks, were used. The biomass samples were characterized by infrared spectroscopy (FTIR), X-ray diffraction and analysis of elemental composition. Among all maize stover fractions, stalks showed the highest C:N ratio, degree of crystallinity and cellulose and lignin contents. The high crystallinity index of stalks (38%) is associated with their high cellulose content (44.87%). FTIR analysis showed that the spectrum of maize stalks is characterized by the highest intensity of bands at 1512 cm−1 and 1384 cm−1, which are the characteristic bands of lignin and cellulose. Obtained results indicate that the maize stover fraction has an influence on the chemical and structural parameters. Moreover, presented results indicate that stalks are characterized by the most favorable chemical parameters for biogas production.