The aim of this study was to investigate the effect of a variety of phenolic type antioxidant additives on the microbial stability of biodiesel and diesel/biodiesel blends. Six synthetic phenolic type antioxidant agents were added in FAME at concentrations up to 1000 ppm. Treated FAME was also blended with Ultra Low Sulfur Diesel (ULSD) fuel at a concentration of 7% v/v in order to examine the activity of the substances in the final blends. The oxidation stability in the presence of the phenolic compounds was determined by carrying out measurements under accelerated oxidation process in the Rancimat unit. The effectiveness of those antioxidant agents against microbial contamination in biodiesel fuel was studied under certain testing protocols for detecting microbiological activity in the fuel supply chain and for evaluating antimicrobials against fuel bio-deterioration. In order to examine the relative activity of those phenolic antioxidants on the microbial stability of FAME and their B7 blends, the study was divided in two parts. During the first part, the ability of the additives to have an inhibitory effect on the growth of microorganisms was evaluated. Following to this and based on the results from the initial stage, the additives’ effectiveness in suppressing microbial activity in challenged laboratory-scale microcosms was assessed by monitoring the alterations in the active bioburden over a period of one month. Overall, the results demonstrate that certain phenolic antioxidants primarily added to FAME in order to improve the oxidative stability could also enhance the microbial stability of the fuel.