The performance of microbial fuel cell (MFC) highly depends on the selection of appropriate electrode materials, in particular – cathodes. Herein, two different activated carbons (CWZ-22 and CWZ-35) without binder, as well as the activated carbon modified with silica nanoparticles (CWZ-22/Si), were used to improve the performance of air cathodes. Nearly one year of operation of materials varying in surface area and microporous structure revealed significant differences in their dynamic behaviour. CWZ-22 with lower surface area and a smaller micropore size, reached an internal resistance (Rint) of 162 Ω, and a maximum power density of 23.3 W m−3. CWZ-22/Si, coated with silane-siloxane-based silicone microemulsion displayed a drop of maximum power generation by 10%. CWZ-35, with higher surface area, but also higher micropore size, displayed 22.8 W m−3 and Rint of 159 Ω. The monitoring of electrochemical and performance parameters indicated an improved long-term behaviour of the cathodes in the following order: CWZ-22 > CWZ-22/Si > CWZ-35. This is the first work in which the pore size distribution and surface area are demonstrated to have a long-term impact on cathodic fouling, and, depending on these properties, this impact may be either positive or negative on MFC performance.