Bioactive small molecules (BSM), produced by natural resources (microorganisms and plants), are extensively used in research and development in academia, biotechnology and pharmaceutical industry and in diagnostics. Development of BSM is a complex task which begins with identification of the ideal microorganism, understanding its nature and optimal culture conditions to allow production of the BSM of interest. Even then a BSM can often be described as a needle in a hay stack and needs to be pulled out, identified and purified. Most of the processes described herein end up in relatively small scales (a few liters) yielding at the most gram quantities of the BSM of interest. Here we describe the long course of challenging development and up-scaling process of a few BSM (Apoptolidin, Cyclosporin A and Fumonisin B) which ended up with great deal of success.