The aim of this study was to monitor the fatty acids and biogenic amines (BAs) profiles in mullet (Mugil Cephalus) and tuna (Thunnus thynnus) roe (bottarga) during storage (0–180 days) at 4 °C. Fatty acids were analyzed by gas chromatography (GC) as methyl ester derivatives while BAs were investigated using reverse-phase liquid chromatography (RP-LC) as dansyl derivatives. The content of total fatty acids decreased with time in mullet bottarga (BM) while in tuna bottarga (BT) the PUFA value showed a slight decrease up to 30 days followed by an intense reduction after 90 and 180 days. An increasing content of BAs was observed with time in all investigated samples without reaching hazardous concentrations. In general, the BAs concentrations were in decreasing order: tyramine, putrescine, cadaverine and histamine. In BM, phenylethylamine was always present, representing a possible discriminating compound as it was absent in tuna bottarga at any time of storage. A Pearson correlation matrix showed that lipid and protein degradation products were strongly and significantly correlated over the considered storage time implying that lipid oxidation processes are in some way linked to the chemical production of BAs.