Today, it is clear that the study of malacological remains in archaeology has a great potential to reconstruct techno-economic, social, and territorial patterns in the past. In recent years, pioneering research has set a methodological basis for the study of shells from a behavioural perspective. However, taphonomic bias is still poorly understood. In this paper, we present the results of the first phase of the ArchaeoENHANCE project developed within the International Research Network of Taphen (CNRS). A long-term experimental protocol was designed and implemented to improve the systemic comprehension of the malacological collections in archaeological contexts, especially focusing on taphonomic causes and effects in macro and microscopic analyses. The results of the analysis after eighteen months of shell burial show an unequal development of alterations among the different taxa selected for the project (Patella, Mytilus, Glycymeris and Callista chione). Among taphonomic alterations, mechanical processes are significant, as is dissolution. Although the experimental protocol is still in its first phase, the results show the need for similar long-term projects. We expect that the extension of the experimental protocol will improve the understanding of the effects of taphonomic modifications on archaeomalacological assemblages, which is of interest for elucidating assemblage formation processes and their interpretation.