The noble pen shell (Pinna nobilis), the largest bivalve of the Mediterranean Sea, plays a crucial role in marine ecosystems as a habitat builder. Its population has suffered massive die-offs due to the parasite Haplosporidium pinnae and bacteria, beginning in 2016, resulting in the species being listed as endangered. This paper investigates the diversity of macrofauna inhabiting the empty shells of noble pen shells in two bays on the western coast of Istria: Valovine Bay and Soline Bay. The research was conducted over four seasons and included a comparison of organisms in upright and horizontal shells. A total of 195 animal species from 19 taxonomic classes were identified, with an average abundance of 28.58 organisms per shell. Statistical analyses revealed significant differences in the number of organisms between bays and across seasons, with Soline Bay harboring more organisms than Valovine Bay. It was also found that upright shells hosted more organisms than those lying flat. Species from the classes Malacostraca, Bivalvia, and Gastropoda were among the most abundant and dominant. The most numerous species were the decapod Pisidia bluteli, the polychaete Sabella spallanzanii, and the bivalve Rocellaria dubia. The analysis also indicated the impact of seasonal changes on organism abundance and diversity. An increase in the number of organisms and species richness was observed with decreasing temperatures and eutrophication in Soline Bay. The importance of empty pen shells in the ecosystem is demonstrated by their role as habitats for numerous marine organisms, including endangered species like the marbled electric ray (Torpedo marmorata). Plastics, primarily fishing gear debris, were also found in the shells, particularly during the summer months. The results of this study highlight the importance of preserving pen shells, not only for their role during their lifetime but also for their function after death as habitats that significantly contribute to biodiversity on sedimentary sea bottoms.