This study was to examine the effect of microbial formulation on converting mill mud (organic waste generated during the clarification of sugar-cane juice in sugar cane industry) into upgraded fertilizer. Pot-culture experiment was performed using sandy loam as the potting matrix and tomato as the test plant. Four treatments were tested in this study: samples of mill mud from two sources (FV-Mill Mud and FC-Mill Mud) and formulated prototypes using the two mill mud samples plus our microbial formulation (FV-NS-1 and FC-NS-1S). On day 13, tomato seedlings from the FV-NS-1 treatment were statistically significantly taller than the other treatments. On day 43, seedlings treated with the formulated prototypes (FV-NS-1 and FC-NS-1S) had significantly larger crown diameter, plant height and chlorophyll content than the counter raw material treatments (FV-Mill Mud and FC-Mill Mud). Seedlings with FV-NS-1 and FV-Mill Mud treatments were significantly larger than those with FC-NS-1S and FC-Mill Mud, respectively. At harvest, significantly better growth of the tomato seedlings was observed in the sequence of FV-NS-1 > FC-NS-1S>FV Mill Mud > FC-Mill Mud. This study has demonstrated that use of well-designed microbial formulation can significantly enhance mill mud’s fertility. In addition, the results have also illustrated that FV-Mill Mud can enhance plant growth significantly better than FC-Mill Mud, suggesting that mill mud quality is also one of the factors affecting the performance of the final fertilizer products.