This work reports an analytical study conducted prior to the conservation intervention of a collection of elephant tusks excavated from a wreck site of a 600–500 BC Phoenician trading vessel in Bajo de la campana (Murcia, Spain). The conservation state of ivory, determined by prolongated immersion in a marine environment, was established by a multi-technique methodology: light microscopy, field emission scanning electron microscopy–X-ray microanalysis (FESEM–EDX), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), spectrophotometry and gas chromatography–mass spectrometry (GC–MS). The analyses demonstrated that the structure and composition of both tusk parts, namely the inner ivory and outer cementum, were altered due to characteristic diagenetic processes of a marine environment. Ca enrichment was observed in both tusk parts, which gave higher Ca/P molar ratio values than for ideal hydroxyapatite. Mg leaching was observed, together with uptake of exogenous elements (F, Cl, Si, Al, S, Na, Fe, Cu, Sr, Pb, Sn, Ag, V, Ni, Cd and Zn), which were prevalently identified in the external tusk part. Uptake of S and Fe was associated with the neoformation of pyrite framboids. The high carbonate content measured by FTIR, which agreed with the higher Ca/P ratios found in the archaeological tusk, was ascribed to the carbonate substitution of phosphate groups (type-B) in the bioapatite accompanied by some authigenic calcium carbonate that infilled ivory. An increased degree of crystallinity was observed when comparing the values of several crystallinity indices found in the archaeological bioapatite with those of a modern tusk, used as the reference material. Increased crystallinity prevalently took place in the cementum. In accordance with increased crystallinity, the HPO42− content index indicated that the hydrated layer of bioapatite nanocrystals diminished in the archaeological tusk, and prevalently in the cementum. All these changes correlated with the significant organic matter loss reported for the archaeological tusk. Interestingly, remaining collagenous matter noticeably altered with enrichment in glycine and depletion in acid amino acids. Changes in the secondary structure of proteins were also recognised and associated with collagen gelatinisation. In addition to proteinaceous materials, small amounts of long-chain fatty acids, monoglycerides and cholesteryl oleate were identified by GC–MS. Cholesteryl oleate was associated with blood, which could have precipitated at the time of specimen death. The identification of large amounts of pyrite framboids and the high oleic acid/palmitic acid ratio in the archaeological tusk suggested minimal oxidative degradation processes, probably due to the slightly anoxic conditions of the underwater Bajo de la campana site environment.