Ceramic fragments from the Islet of Guidoiro Areoso (NW Spain), covering a wide range of cultural periods (Neolithic to Late Bronze Age), have been studied by color analysis, elemental analysis of carbon (C) and nitrogen (N), and molecular analysis (thermally assisted hydrolysis and methylation, THM-GC-MS), in order to identify the organic matter (OM) in the prehistoric pottery and reveal information on ceramic production techniques, food remains and post-depositional effects. Results showed that the strong marine influence (sherds recovered from coastal deposits) and microbial activity (recovery from waste deposits, “cuncheiros”) had a profound effect on C/N ratio and molecular composition (N-rich protein and chitin structures). Other organic ingredients originated from the material used for creating the ware (detected as pyrogenic OM) and possibly food remains (fatty acid fingerprints). Dark-colored ware was enriched in both pyrogenic OM from incomplete combustion and non-bacterial fatty acids. Fatty acid patterns could not be related to possible vessel use, and markers of aquatic resources were scarce, or absent. It is argued that THM-GC-MS of pottery fragments is useful for understanding how an archaeological deposit developed in time, what kinds of OM are present, and possibly to make a pre-selection of samples with high potential for more cost-demanding dietary molecular assessments.