A method and apparatus for the regeneration, acclimation and conditioning of in vitro derived plant propagules is presented. The apparatus comprises a regulated chamber, a laminar flow work station coupled to the regulated environment, and a supply compartment. A process control system regulates the chamber to sterile or near sterile conditions. The process control system monitors and modulates the microenvironment, nutritional profile and frequency of fertigation, atmospheric composition, as well as the quality and quantity of irradiance incident on propagules in the sterile chamber. This controlled environ optimizes propagules regeneration, and facilitates the establishment of photoautotrophism and homeostatic capacity of plant tissues. Furthermore, the apparatus allows for the metabolic and morphologic conditioning of plantlets for high intensity indoor cultivation as well as the inoculation of plantlets with beneficial bacteria and fungi which increase metabolic function and provide a protection from colonization of plantlets by pathogenic microflora through spatial occupation.