Our research demonstrates that the extent of isoleucine epimerisation (A/I) in fragments of avian eggshells provides geochronological information in archaeological contexts. In the archaeological sequence of Hay Cave, northern Queensland, Australia, there is an excellent correspondence between the A/I values of Australian brush-turkey (Alectura lathami) eggshells (n = 99) and independent geochronological control (n = 16 radiocarbon ages including 4 on eggshell calcite). The A/I values identify three phases of deposition during the Holocene at Hay Cave. In contrast to the Alectura eggshell A/I values, a poor correspondence was observed between the A/I values of cassowary (Casuarius) eggshells from Toe (n = 35) and Kria caves (n = 23) (Ayamaru Plateau, Papua) and the depths from which the specimens were recovered in these stratified sequences. Given coherent archaeofauna trends and radiocarbon chronologies (n = 8 and 2 eggshell calcite radiocarbon ages at Toe and Kria, respectively) with respect to depth, the variable A/I values are not explicable in terms of mixing. Rather, the variability is most likely due to exposure of the eggshells to the high temperatures of campfires. Despite the variability, eggshells with relatively low A/I values amongst specimens recovered from similar depths (and therefore presumably least influenced by high temperatures) exhibit a gradual increase in A/I with respect to depth, as expected in a stratified deposit. From this observation it is suggested that the identification of heated eggshells will increase confidence in geochronological information provided by A/I. These studies illustrate the complications that arise from campfire-induced acceleration of amino acid racemisation and emphasise that although this phenomenon is common, it is not universally encountered in archaeological contexts.