Although it has been almost twenty years since the discovery of the now classic and widely-used Brust–Schiffrin two-phase method (BSM) for synthesizing organothiol-stabilized metal, chiefly Au, nanoparticles (NPs), details in terms of the metal NP formation mechanism have not yet been fully unravelled. It had long been accepted that Au ions form polymerized species with organothiol molecules before being reduced and forming zero valence Au0 NPs in the BSM synthesis. But recent studies have discovered that the BSM is fundamentally an inverse micelle based process in which the phase transferring surfactant TOAB (tetraoctylammonium bromide) first forms inverse micelles inside the organic phase where water and transferred Au ions are loosely encapsulated, with a structure that can be expressed as [TOA][AuX4] (X=Cl− and/or Br−). It turns out that this inverse micelle structure and the water it encapsulates play key roles in the formation of Au NPs. In this chapter, we will review and discuss in various degrees of detail the relevant chemistry involved in the BSM synthesis of alklychalcogenolate-stabilized metal NPs and highlight the similarity and difference when ligands containing different chalcogen elements (S, Se, or Te) are used as the starting source of the NP-stabilizing agents.