Pyrolysis gas chromatography–mass spectrometry (Py–GC–MS) analysis of Neolithic (4900–3800 BC) archeological rice grains (husked rice fruit) from the Tianluoshan site (Zhejiang Province, eastern China) revealed no polysaccharide products from starch present in the original rice fruit; however, benzene, toluene, dimethyl benzene, phenol, dimethyl phenol and n-alkanes > C30 were detected, indicating their aromatic nature, plus some aliphatic components. On the contrary, polysaccharides were observed in husk material but in significantly lower concentration than in the modern equivalent. The molecular composition was supported by 13C nuclear magnetic resonance spectroscopy (NMR) data. Variation in preservation quality was also detected in persimmon seeds, oak acorns and amanranthaceous seeds from the site. This variation in molecular preservation, which could also be observed at the micro-morphological level, was tracked with scanning electron microscopy (SEM). Variation in bulk tissue carbon isotopic values (d13C) was apparent among archeological samples, a net 1–2‰ positive shift in bulk tissue d13C being found in most of the Tianloushan plant remains. Our data suggest the importance of post-excavation storage conditions and illustrate the power of the application of multiple analytical methods for the study of archeological plant remains.