Towards the commercialisation of microbial fuel cell (MFC) technology, well-performing, cost-effective, and sustainable separators are being developed. Ceramic is one of the promising materials for this purpose. In this study, ceramic separators made of three different clay types were tested to investigate the effect of ceramic material properties on their performance. The best-performing ceramic separators were white ceramic-based spotty membranes, which produced maximum power outputs of 717.7 ± 29.9 µW (white ceramic-based with brown spots, 71.8 W·m−3) and 715.3 ± 73.0 µW (white ceramic-based with red spots, 71.5 W·m−3). For single material ceramic types, red ceramic separator generated the highest power output of 670.5 ± 64. 8 µW (67.1 W·m−3). Porosity investigation revealed that white and red ceramics are more porous and have smaller pores compared to brown ceramic. Brown ceramic separators under performed initially but seem more favourable for long-term operation due to bigger pores and thus less tendency of membrane fouling. This study presents ways to enhance the function of ceramic separators in MFCs such as the novel spotty design as well as fine-tuning of porosity and pore size.