This paper explores the full potential of archaeobotanical research in the investigation of issues such as agricultural practices and resource management and mobilisation in shaping the social dynamics of Neolithic and Bronze Age Crete, through a synthesis for the first time of all available archaeobotanical information to date. To this body of data new information is added from six sites: Kephala Petras, Pryniatikos Pyrgos, Aghia Fotia, Knossos Little Palace North, Sissi and Zominthos. A comprehensive methodology is devised using three units of analysis to allow an in-depth study, firstly of the quality of the available dataset and secondly of its content. A total of 80 archaeobotanical records, compiled in one database, are examined in the light of the methods employed for their sampling, recovery and processing. The reliability of the current dataset is assessed, highlighting shortcomings; methodological issues are addressed to improve its quality. These records are then analysed according to their temporal, spatial and contextual distribution across the island. A synthesis of the full resource base, including cereals, legumes, fruits, nuts, condiments and wild species, is conducted, providing a contextualised picture of their availability and use, and identifying lacunae and interpretational potential. On these bases a research agenda is set and future research priorities and new approaches are suggested that place archaeobotany in the core of current archaeological discourse on social models, practices and meanings for prehistoric Crete.