Fast, sensitive nucleic acid sensors that enable direct detection of bacteria and diagnosis of infectious disease would offer significant advantages over existing approaches that employ enzymatic amplification of nucleic acids. We have developed chip-based microelectrodes that are highly effective for bacterial detection and have shown that they can capture and permit the analysis of large slow moving mRNA targets. Here, we explore new approaches to tune their analytical sensitivity and investigate the effect of sensor size, material composition, and probe density on the electrochemical signals obtained in the presence of bacteria. Sensor size can be varied from 10 to 100 μm, and this parameter can change detection limits obtained by a factor of 100. Changing the surface coating can also be used to tune sensitivity, with more nanostructured coatings yielding the most sensitive detectors. Moreover, we assessed performance of the sensors by tuning probe density. Varying the density of the immobilized probe had a dramatic effect on sensitivity, with sparse probe monolayers providing superior levels of performance. Overall, this study points to several factors that can be used to tune detection limits.