To help design bacteria-friendly anodes for unmediated benthic microbial fuel cells (MFCs), we explore the role of anatase TiO2(101) surface biocompatibility in selecting the functional groups of the levo-isomer serine (L-Ser), which contains carboxyl, hydroxyl, and amino groups in a single molecule. By performing total energy calculations and molecular dynamics simulations based on a density-functional tight-binding method, we find that at room temperature, the surface should be active for biomolecules with carboxyl/carboxylic and hydroxyl groups, but it is not sensitive to those with amino groups. The hydrogen bonding between the hydroxyl H and surface O facilitates electron transfer from the pili or the bacterial matrix to the anode surface, which improves the output power density. Thus, in combination with conductive polymers, the anatase TiO2(101) surface can be an effective biocompatible substrate in benthic MFCs by enabling the surface O to form more hydrogen bonds with the hydroxyl H of the biomolecule.