The ‘hilly flanks’ of the Zagros in the eastern Fertile Crescent (EFC) were the first area explicitly targeted for investigating the emergence of agriculture and sedentary life starting in the late 1940s. The subsequent concentration of research on the Levant and Anatolia suggested that early Neolithic innovations initially emerged in the western and central areas of the Fertile Crescent. However, renewed work in the central Zagros has once again highlighted this region as a key region in a wider cultural mosaic that witnessed local developments of the neolithisation process. To provide new impetus for investigating the transition from the Late Pleistocene to the Early Holocene in the EFC, we summarise here the results of the joint Iranian-Danish Tracking Cultural and Environmental Change project, as part of which the Neolithic sites of Asiab and Ganj Dareh and the Epipaleolithic cave site of Mar Gurgalan were re-excavated using current methods and techniques. Although both Asiab and Ganj Dareh were previously excavated quite intensively, the lack of publications on both sites and advances in archaeological methods since their initial investigation left many questions unanswered. In addition, the excavation of Mar Gurgalan provided an opportunity to investigate the Epipaleolithic period of the central Zagros in greater detail. In addition to summarising the results of our work at these sites, we will therefore also contextualise them before the background of broader debates concerning the emergence of Neolithic societies in Southwest Asia.