The main goal of this paper is to explore possible cultural continuities and discontinuities at the Neolithic transition in Eastern Iberia. To address this issue, we introduce a twofold methodology, consisting of Geometric Morphometrics and the use of the self-developed Geomeasure system, to examine evolutionary patterns in geometric microliths. These are a specific type of arrowhead shared by both the last hunter-gatherers and the first farmers from two reference sites in the region: Cueva de la Cocina and Cova de l’Or (Eastern Iberia). Although advances in research have contributed to a better comprehension of this process, there are still unanswered questions, especially when the study is approached from a regional perspective. Such is the case for the Neolithisation of the Eastern Iberian Peninsula, and the way in which the previous Mesolithic population interacted—if they interacted at all—with the first farmers. In this case, some sites present archaeological contexts that have been catalogued as acculturation contexts. This has traditionally been the case for phase C of Cueva de la Cocina (Spain), although recent research points to the possibility that the content of this specific deposit is the result of post-depositional processes. Here we try first to understand the cultural evolutionary patterns and relations between the different geometric microlith technocomplexes and, second, to address the specific problem of the interpretation of taphonomic disturbances in the archaeological record. We use the Cueva de l’Or and the Cueva de la Cocina for comparison, and our conclusions raise serious doubts about the existence of an acculturation phase at the latter.