Microbial fuel cells (MFCs) are an alternative electricity generating technology and efficient method for removing organic material from wastewater. Their low power densities, however, hinder practical applications. A primary limitation in these systems is the anode. The chemical makeup and surface area of the anode influences bacterial respiration rates and in turn, electricity generation. Some of the highest power densities have been reported using large surface area anodes, but due to variable chemical/physical factors (e.g., solution chemistry, architecture) among these studies, meaningful comparisons are difficult to make. In this work, we compare under identical conditions six micro/nano-structured anodes in micro-sized MFCs (47 μL). The six materials investigated include carbon nanotube (CNT), carbon nanofiber (CNF), gold/poly (ϵ-caprolactone) microfiber (GPM), gold/poly(ϵ-caprolactone) nanofiber (GPN), planar gold (PG), and conventional carbon paper (CP). The MFCs using three dimensional anode structures (CNT, CNF, GPM, and GPN) exhibited lower internal resistances than the macroscopic CP and two-dimensional PG anodes. However, those novel anode materials suffered from major issues such as high activation loss and instability for long-term operation, causing an enduring problem in creating widespread commercial MFC applications. The reported work provides an in-depth understanding of the interplay between micro-/nano-structured anodes and active microbial biofilm, suggesting future directions of those novel anode materials for MFC technologies.