Different nanoscopic paths to witherite nanoparticle formation via the birth and deterioration and/or transformation of meta-stable amorphous and, so far unreported, crystalline barium carbonate nanoparticles using nonionic water-in-oil microemulsions as precipitation media have been investigated in detail by transmission electron microscopy (TEM) and selected area diffraction (SAD). Compared to precipitation from homogeneous media, employment of microemulsions allows for a more precise control of the ongoing nucleation and growth processes - not only via adjusting the concentration of the reacting species involved and temperature - but also by tuning the size and the exchange kinetics of the isolated and compartmentalised nanometre-sized water domains. Here we present a comprehensive study on how tuning the properties of the parental microemulsion can be implemented in tailoring the crystal structure, morphology and self-assembling properties of nucleating and growing nanoparticles. At low water content a variety of different meta-stable nanoparticles forms that ranges from in the electron beam amorphous (a) filaments to monoclinic (m) cubes and hexagonally shaped, probably trigonal (t), thin platelets, which assembly into micrometre-long stacks. Slowing down of the exchange kinetics permits us to study the early stages of particle formation and to gain full insight into unrevealed crystal transformation and re-crystallisation processes. The genesis of the, at ambient conditions thermodynamically stable, orthorhombic (o) polymorph (witherite) evolves either via direct transformation (e.g. a→o transition from filaments into rods) or via dissolution/re-crystallisation processes. In the latter case the crystalline pre-structure particles dissolve, thereby freeing material for the re-nucleation of the witherite phase (m/t→o transition), emphasising the double role of the microemulsion domains as nucleation site and host for water-soluble species. Depending on the different crystallisation paths taken and the growth conditions, a rich variety in final nanoparticle morphologies is obtained.