The performance of sediment microbial fuel cells (SMFCs) is usually limited by the structure, moisture, and salt content of the soil where they are allocated. Despite the influence of soil, so far most of efforts to improve SMFCs have been limited to the hardware design of the bioelectrochemical device. Our main objective was to enhance performance of SMFCs by stimulating the in situ formation of silica colloids in a low conductivity rice paddy soil. Our results have revealed that the presence of a silica colloid network, described by cryo-SEM analysis, reduced soil resistivity, enhanced ion mobility and consequently enhanced the power production by a factor of 10. Furthermore, our silica-supplemented soil showed better utilization of the electron donor, either acetate or natural rice root exudates, by electrogenic microbial populations. Sustainable manipulation of soil micromorphology using environmentally friendly reagents such as silica offers a novel approach for enhancing the performance of in situ microbial electrochemical applications in low conductivity soils, thus silica colloid geoengineering should be considered as part of future applications of SMFCs.