The impressive increase of performance and versatility of the MS-instrumentation, which today represents an indispensable tool in proteomics, has determined a considerable growth of the so-called paleoproteomics as interdisciplinary approach, which involve chemists, archaeologists, and evolutionary biologists. Archaeological proteins residues can inform us about production, use, state and preservation of a material, about evolutionary and ecological divergences, dietary habits and past cultures. This paper reports the results of the characterization of proteins extracted from the pottery of the Maltese site of Baħrija, the guide-site for the local Iron Age (11th-8th century BCE). Proteomic data here reported confirm that one the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. In this context, the lack of archaeozoological and paleobotanical data for the settlement at Baħrija makes the outcomes of the proteomic analysis even more relevant in terms of contributing to reconstruction foodways and dietary habits of that ancient community. Particularly, our data revealed that wheat turned out to be a cereal used in the diet of the ancient community of Bahrija.