Plant tissue culture is an important biotechnological tool, which involves biochemical and genetic manipulations to onset specifi c gene programming, which determines an optimal cell differentiation state for the production of bioactive compounds. Indeed, not only the metabolism but also the morphogenetic processes are modifi ed in plant cells to drive the synthesis and accumulation of economically valuable compounds. In this chapter, we provide an overview of the current molecular approaches to control the expression of specifi c genes encoding putative heterologous and native enzymes as well as transcription factors to enhance the metabolic fl ow of specifi c pathways in order that notable bioactive compounds can be accumulated in plant cells at acceptable commercial levels. Such methods vary from singlegene plant transformations to the emerging multi-gene transformation (gene stacking) technologies embraced by private companies focusing primarily in the metabolic engineering of secondary metabolism. The virtues and potential of these molecular methods in their application to tissue culture systems are presented. Additionally, the importance of subcellular targeting of proteins, notably biosynthetic enzymes and pharmaceutical antibodies, for enhancing their activity and stability is also discussed. Finally, the progress in two emerging approaches for the production of bioactive molecules, the manipulation of cell differentiation and cell immortalization are expounded in this article. Thus, we present the molecular basis to control both cell differentiation and cell immortalization in plant tissue culture systems as novel avenues to control and perpetuate the gene programming which in turn creates and regulates cellular microenvironments for the optimal biosynthesis of valuable compounds. Consequently, our objective is to present how basic approaches, including the manipulation of gene expression, are amalgamated to other molecular strategies of higher hierarchy, particularly the manipulation of cell differentiation and immortalization for the synthesis of bioactive molecules in plant tissue culture platforms.