Toxoid vaccines are used routinely in the livestock industry to prevent animal-disease caused by pathogenic clostridia. Clostridium toxoid vaccines are produced using batch fermentation processes with complex mediums, and the produced toxin is then inactivated with formalin to form the toxoid. However, the lack of industrial process reproducibility due to media preparation and composition results in random titres and sporadic batch failures, causing great economic losses. Here, we applied a systems biology approach to study Clostridium tetani potent neurotoxin production, responsible for the life-threating tetanus disease. We show that time-course transcriptomics and metabolomics data allowed discovering key components in toxin production regulation. We initially found that the addition of these five metabolites to the medium inhibited toxin production. However, the optimization of each component concentration resulted in a two-fold increase in toxin production. Our results demonstrate that toxin expression is tightly regulated by these components, as small changes in the metabolites concentration drastically changed from toxin inhibition to high productivity. We anticipate that these findings will help the industry to achieve much higher titres than those obtained today and to restore poor batches performance.