Bottarga is a high-priced delicacy with high nutritional value, and, in Italy, bottarga from mullets has been recognized to be a traditional food product. The flathead grey mullet Mugil cephalus and the thinlip grey mullet Liza ramada are the main cultured grey mullets in the Mediterranean Sea. In this study, fresh roe and bottarga from these two species were investigated to evaluate the influence of the technological process and the species on their biochemical composition and health advantages. The 1 h/200 g salting-out step did not increase the levels of NaCl in the bottarga, although it highly decreased the levels of some heavy metals like Cu and Al. Processing of fresh roe in bottarga led to an essential modification of the lipid fraction, following a general series of monousatturated fatty acid (MUFA)> poliunsutturated fatti acid (PUFA) > saturated fatty acid (SAFA) and an increase in both ω3 and ω6 in Liza ramada. Moreover, bottarga showed higher levels of squalene and cholesterol and an increased Essential Amino Acid/Total Amino Acid ratio (EAA/TAA) in both species. In addition to the nutritional benefits for the consumer, the process proposed in this study may represent a reliable tool for local producers to obtain a final bottarga with both a reproducible biochemical composition and organoleptic characteristics.