The future extraction of deep-ocean mineral deposits depends on being able to recover the metals in an economic and environmentally sensitive way. Metal production is one of the most energy intensive industrial sectors. The characteristics of some deep-ocean mineral deposits permit them to be readily dissolved and to release their contained metals into solution. Current innovations in hydrometallurgy, including metal leaching with ionic liquids and solvent extraction in non-dispersive phase contactors, demonstrate how metals could potentially be extracted from Fe–Mn deposits with increased energy efficiency and a reduced environmental footprint compared with traditional processing techniques. The importance of biological processes in the formation of deep-ocean Fe–Mn deposits is poorly understood. However, understanding how microorganisms select and deposit metal ions could further enhance targeted extraction of ‘critical’ metals.