Biotechnological production of omega-3 polyunsaturated fatty acids (PUFAs) has become a commercial alternative to fish oil in the past twenty years. Compared to PUFA production by fatty fishes, that from microorganisms has increased due to its promising sustainability and high product safety and to increasing awareness in the expanding vegan market. Although autotrophic production by microalgae seems to be more sustainable in the long term, to date most of the microbial production of omega-3 is carried out under heterotrophic conditions using conventional fermentation technologies. The present review critically analyzes the main reasons for this discrepancy and reports on the recent advances and the most promising approaches for its future development in the context of sustainability and circular economy.