Biodiesel is commonly produced via the transesterification process, usually through the use of batch type reactor. There are significant gaps in batch reactor technologies, where the importance of these factors are often concluded based on the steady-state conditions, manifested in the form of the final yield. In this study, a comprehensive test matrix is setup using full factorial design of experiments, consisting of 4 factors and 2 levels. Four parameters of interest such as agitation speed (200-400 rpm), catalyst loading (0.5-1.5 wt%), methanol to oil ratio (3:1-6:1), and temperature (30-60 °C), were investigated to understand the interaction of these independent factors at the different stages of transesterification. To further investigate the effect of each factors on the transient process, one-way effect of these factors on the transient yield is investigated. Through the multi-factor analysis, the transesterification process can be segregated into 5 unique stages, as the standardised effect of these factors responded differently throughout. The results indicate that batch reactor transesterification performs better with low methanol-oil ratio at the beginning phase, and importance of methanol-oil ratio significantly increases over time. The methanol-oil ratio also become the most influential factor when steady-state is achieved, from a standardised effect magnitude of 0.38 to 14.21, representing an over 37-fold improvement. Agitation speed also showed a reduction of 37-fold in standardised effect throughout the transesterification process, where the effect reached plateau around mid-way of the reaction. Catalyst loading and temperature share similar trends, as they both influence the activation energy of transesterification. Although catalyst loading and temperature are highly influential throughout, a 1.88 and 1.78fold decrease in impact are observed. In conclusion, this study provides insights towards developing biodiesel production techniques, through better understanding of the cross-interactions between factors, and in terms of optimising transesterification dynamically.