Most of concrete structural failures are attributed to poor workmanship and poor engineering designs. Some microorganisms present in sewer systems can degrade the concrete and/or mortar. Concrete failures due to microbial attack has not attracted much attention especially in developing countries such as Kenya. This study investigated the effect of Thiobacillus intermedius bacteria on the performance of Ordinary Portland Cement (OPC). Preparation of test mortar prisms was done using the bacterial solution as either mix water, curing water or both. The control mortar prisms were prepared and cured in distilled water. Compressive strength test was done after 7th, 28th, 56th and 90th days of curing respectively. Results showed significant drop in compressive strength for the mortar prisms prepared and cured in bacterial solution as compared to the control mortar samples. Soundness and normal consistency increased significantly for the bacterial treated cement paste as compared to the control sample. Scanning Electron Microscopy (SEM) analysis showed severe damage on the bacterial treated cement mortar. This was characterized by formation of deleterious expansive products like ettringite and gypsum. Control mortar sample exhibited even formation of hydration products within the pore system.