A sensitive and selective gas chromatography-tandem mass spectrometry (GC–MS/MS) method for the detection and quantification of terpenes, monoterpenoids and alkanes was developed and validated, to complement an existing analytical workflow set up for organic biomarker analysis of stone artefacts. This method was applied to seven stone artefacts—six of which contained potential use-residues based on a previous study using non-volatile low molecular weight lipid biomarkers—recovered from Liang Bua, an archaeological cave site on the Indonesian island of Flores. Following localised solvent extractions of the artefacts, aliquots of the solvent extracts were directly assayed using the optimised method. Identification of an analyte was considered positive when three criteria were met: (1) the retention time was the same as observed for a reference standard; (2) the three selected multiple reaction monitoring transitions for a reference standard compound were observed for the analyte; and (3) the qualitative ions (relative to the quantitative ion) were present in the expected ratios consistent with the reference standard. Alkane chemical profiles indicated that the presence of plant residues cannot be excluded, but of particular interest was the detection of camphor on one of the artefacts. Camphor-containing plants are found throughout Asia, including Indonesia, and are known historically to have been used for medicinal and culinary purposes. The likelihood of resource processing was high for three of the artefacts, and medium for the remaining four artefacts, based on the specificity, quantity and combination of the analytes identified.