It is of fundamental importance in forensic entomology that the factors controlling carcass temperatures during decomposition are thoroughly understood. The thermal environment to which fly larvae are exposed is the primary influence on their growth rate, and hence affects any estimate of minimum time since death using such specimens in homicide investigations. To date, much of the entomological research on maggot masses has focused on their elevation of carcass temperatures, with very little focus on the bacteria associated with larval activity. The aim of this study was to investigate the heat associated with decay and the types of bacteria present during the decomposition of a carcass, both in the presence and in the absence of maggots. Three treatments were imposed: fresh, frozen and maggot-infested, each consisting of five replicate pig carcasses. Temperature measurements and bacterial swabs were taken from the gastro-intestinal region of each pig and temperatures and bacterial communities compared between treatments. All carcasses reached average maximum temperatures above 32 °C in a temperature controlled room set at 23 °C. Treatment had no statistically significant effect on the temperatures recorded in each carcass but did significantly affect the community structure of the bacteria. However, bacterial community structure varied across time. This study suggests that bacterial metabolism plays a significant role in carcass thermogenesis, and that maggot masses, while contributing to localised heating within the carcass, may have less of a role in elevating carcass temperatures than previously assumed.