The compression ignition (CI) engines are most efficient and robust but they rely on depleting fossil fuel. Hence there is a speedy need to use alternative fuels that replaces diesel and at the same time engine should yield better performance. Accordingly, honge oil methyl ester (BHO) and cotton seed oil methyl ester (BCO) were selected as an alternative fuel to power CI engine in the study. In the first part, this paper aims to evaluate best fuel injection timing (IT) and injector opening pressure (IOP) for the biodiesel fuels (BDF). The combustion chamber (CC) used for the study is toriodal re-entrant (TRCC). The experimental tests showed that BHO and BCO yielded overall better performance at IT of 19° before top dead centre (bTDC) and IOP of 240 bar. In the second part, the effect of number of holes on the performance of BDF powered CI engine was studied keeping optimized IT and IOP. The six-hole injector with 0.2 mm injector orifice diameter yielded better performance compared to other injectors of different holes and size tested.