The aim of the study is to identify and determine the role of microbial degradation taking place in dusty deposits in potential threats (i.e., destruction of protective coatings and development of corrosion) to the means of transport in conditions of transshipment of energy biomass. This paper presents the results of research on the impact of powdery fractions of wood biomass and biomass obtained from oil plants in the degradation of paint coatings and corrosion processes. During the research, exposure to simulated port climate, OM, SEM, and EDS studies were used. It has been found that the presence of the fraction containing protein compounds and amino acids (e.g., dust of rapeseed meal) stimulates the growth of microorganisms whose metabolism products favour the destruction of protective coatings and the development of corrosion. Under the same conditions, the destruction of protective zinc coatings has been observed. It was found that already 14 days of exposure to oily biomass deposits results in damage to paint coatings caused by microbiological processes. The 8-week exposure causes serious degradation of protective coatings and the base material itself. The biomass of wood origin, containing compounds of the tannin type, did not show as much aggressive activity as the biomass with protein compounds.