The diesel fuel supply chain faces new challenges associated with microbial contamination symptoms in biodiesel fuel. FAME's (Fatty Acid Methyl Esters) chemical composition along with its hygroscopic nature makes it more “biologically active” and as a result the final blends could be more prone to microbiological contamination. Survey of in-field incidents and facts in the Greek supply chain indicate that biodiesel is more prone to microbial growth. Furthermore, several experimental studies which demonstrate the susceptibility of biodiesel fuel for microbial growth have been conducted in the laboratory. The influence of FAME has been evaluated as well as the effect of microbial proliferation on the quality of the blend. Different types of biodiesel have been blended with Ultra Low Sulphur Diesel at various concentrations, and the resulting blends were mixed with bottom-water of known viable microbial colonies and stored. During storage the microbiological growth was monitored by employing both semi-quantitative and quantitative methodologies. Alterations on the fuel's quality parameters were also examined. The overall observations and results support the rationale for establishing a standard inspection/action plan in the biodiesel fuel supply chain infrastructure, aiming to control and minimize the microbiological growth issues within the context of sustainability.