Nature-based solutions for geotechnical problems are gaining attention across the World. Microbially induced calcium precipitation (MICP) is one among the sustainable solutions. Studies on application of MICP are being extensively carried out on granular soils. However, the studies on influence of clay in calcium carbonate precipitation aided by microbes are limited. The present study focuses on the role of clay content in calcium carbonate precipitation during MICP. In the present study, MICP was carried out on glass beads with varying contents of kaolin and bentonite (0.1, 0.2, 0.3 and 0.4%). It was observed that the presence of clay is beneficial only up to 0.2% of clay content in glass beads. Beyond 0.2% calcium carbonate precipitation was negatively affected. Further, studies were conducted to investigate the effect of surface roughness of substrate in the presence of clay. It was observed that as the surface roughness increases the nucleation sites increases, it increases the quantity of calcium carbonates precipitated aided by microbes.