Bioreduction is a novel method for the on-farm storage of fallen stock in a vessel containing water that is heated and aerated, prior to disposal. The combination of a mesophilic temperature and high bacterial population leads to rapid degradation of carcasses due to microbial and enzymatic breakdown of protein material; and ultimately the reduction in volume of waste to be disposed. The system could, however, be improved if more was known about the changes that occur during a bioreduction cycle. Pig carcasses were placed within two commercial-scale bioreduction vessels (BVs) (6.5 m3 capacity) and the changes in physicochemical parameters, enzymatic activity, gas emissions and microbial communities were analysed over 56 days. Analyses showed that each vessel displayed different physicochemical parameters. The microbial communities within both vessels were also distinct, though they converged between days 28 and 42 before again diverging. Of the enzymes assayed, acetylesterases showed the highest activity during initial stages, with a subsequent increase in lipase towards the end. All other enzymes showed little activity in comparison. Despite active aeration of the vessels, conditions were redox-constrained, leading to the emission of gases associated with anaerobic conditions, namely NH3 and H2S. It was concluded that no single parameter governed the biochemical processes and that each BV will have its own unique microbial population and hence rate of decomposition. Further work is needed to increase the rate of bioreduction through bioaugmentation or developing enzyme additives.