This study provides experimental evidence confirming the significance of microbial mat presence in controlling the spatial and temporal development of chemical microenvironments which become established inside and outside decaying fish carcasses. Dissolved oxygen (DO) and pH profiles were monitored over 1,000 days with microelectrodes positioned inside and adjacent to carcasses. In the vicinity of fish, the DO varied from an oxygenated green upper layer to an anoxic bottom stratum and the pH was alkaline. Inside the fish, the DO and the pH were decoupled during the first week, in that anoxia remained constant and the pH decreased and became acidic. Once covered by the mat, the fish carcass turned oxic and pH returned to alkaline levels. This novel second phase occurred from day 90 to three years and would likely remain after this time. Based on the fish soft tissue quality at the end of the experiment, we discuss whether oxic-alkaline microenvironmental conditions could promote organic preservation and long-term mineralization.