The Atlantis II Deep is a location of modern submarine hydrothermal activity along the slowly spreading Red Sea rift axis. Venting of high-temperature hydrothermal fluids, similar to those associated with black smokers, takes place in a brine pool and has led to the accumulation of 90 Mt (dry, salt free) of stratiform, metalliferous sediment. The conditions of mineralization are unique in the modern oceans, but have been widely suggested as a possible analog of some important ancient stratiform base metal ore deposits. This study shows that many of the proposed genetic models for these ancient deposits may be highly simplified and do not take into account rapid diagenetic transformations, widespread non-equilibrium processes, and many other aspects of metal deposition. Sediment cores of the Atlantis II muds were last studied more than 30 years ago. High-resolution sampling and careful re-examination of the mineralogy and geochemistry of the sediments, using modern analytical techniques has significantly improved the understanding of the different processes responsible for the formation of the finely layered metallifeous sediments. The geochemistry of the individual layers is controlled by highly variable detrital, hydrogenic and hydrothermal input. Primary depositional pathways from the brine pool are the main control on basin-wide metal distribution (e.g., increasing Cu/Zn away from the vents) including variable enrichment in trace metals via scavenging from the brine pool and from the enriched pore waters. Cu and Zn have been deposited not only as sulfides but also with poorly crystalline Si-Fe-(oxy)hydroxides. A significant proportion of the original non-sulfide Cu and Zn are diagenetically transformed into sulfides, but also carbonates and clays, in large part reflecting sulfide deficient pore waters. Negative δ34S values, previously unrecognized in the sulfide- and metal-rich units, indicate a source of bacteriogenic sulfide. Syn-diagenetic processes also appear to have been responsible for the sharp laminations in the sediments, as well as distinctive zoning of carbonate and clay minerals around the vent source. The early diagenetic transformations observed in the Atlantis II Deep may not be preserved in the ancient rock record but nevertheless have important implications for metal deposition in some of the world’s largest and richest base metal ore deposits.