Nearly 55,000 outbreaks of animal disease were reported to the World Animal Health Information Database between 2005 and 2016. To suppress the spread of disease, large numbers of animal mortalities often must be disposed of quickly and are frequently buried on the farm where they were raised. While this method of emergency disposal is fast and relatively inexpensive, it also can have undesirable and lasting impacts (slow decay, concerns about groundwater contamination, pathogens re-emergence, and odor). Following the 2010 foot-and-mouth disease outbreak, the Republic of Korea's National Institute of Animal Science funded research on selected burial alternatives or modifications believed to have potential to reduce undesirable impacts of burial. One such modification involves the injection of air into the liquid degradation products from the 60–70% water from decomposing carcasses in lined burial trenches. Prior to prototype development in the field, a laboratory-scale study of aerated decomposition (AeD) of poultry carcasses was conducted to quantify improvements in time of carcass decomposition, reduction of potential groundwater pollutants in the liquid products of decomposition (since trench liners may ultimately leak), and reduction of odorous VOCs emitted during decomposition. Headspace gases also were monitored to determine the potential for using gaseous biomarkers in the aerated burial trench exhaust stream to monitor completion of the decomposition. Results of the lab-scale experiments show that the mass of chicken carcasses was reduced by 95.0 ± 0.9% within 3 months at mesophilic temperatures (vs. negligible reduction via mesophilic anaerobic digestion typical of trench burial) with concomitant reduction of biochemical oxygen demand (BOD; 99%), volatile suspended solids (VSS; 99%), total suspended solids (TSS; 99%), and total ammonia nitrogen (TAN; 98%) in the liquid digestate. At week #7 BOD and TSS in digestate met the U.S. EPA standards for treated wastewater discharge to surface water. Salmonella and Staphylococcus were inactivated by the AeD process after week #1 and #3, respectively. Five gaseous biomarkers: pyrimidine; p-cresol; phenol; dimethyl disulfide; and dimethyl trisulfide; were identified and correlated with digestate quality. Phenol was the best predictor of TAN (R = 0.96), BOD (R = 0.92), and dissolved oxygen (DO) (R = −0.91). Phenol was also the best predictor populations of Salmonella (R = 0.95) and aerobes (R = 0.88). P-cresol was the best predictor for anaerobes (R = 0.88). The off-gas from AeD will require biofiltration or other odor control measures for a much shorter time than anaerobic decomposition. The lab-scale studies indicate that AeD burial has the potential to make burial a faster, safer, and more environmentally friendly method for emergency disposal and treatment of infectious animal carcasses and that this method should be further developed via prototype-scale field studies.