Self-assembled monolayers (SAMs) modified gold anodes are used in single chamber microbial fuel cells (SCMFC) for organics removal and electricity generation. Hydrophilic (−N(CH3)3+, −OH, −COOH) and hydrophobic (−CH3) SAMs are examined for their effect on bacterial attachment, current and power output. The different substratum chemistry affects both the current and power output and the community composition of the electrochemically active biofilm formed. Of the four SAM-modified anode tested, −N(CH3)3+ results in shortest start up time, highest single electrode polarization and power density, followed by −OH and –COOH SAMs. Hydrophobic SAM decreases bacteria attachment and anodes performance in comparison to hydrophilic SAMs. Electron transfer rate is faster on the N(CH3)3+-surface than on other surfaces, and correlates with a high abundance of δ-Proteobacteria, including electrochemically active species. A consortium of Clostridia and δ-Proteobacteria is found on all the anode surfaces, suggesting a synergistic cooperation under anodic conditions.