Prodigiosin is a red pigment produced by various microbial strains, of these, Serratia marcescens has been recorded as the major PG-producing strain. This microbial pigment has attracted much attention because it possesses potential applications in various fields. Thus, this active metabolite has been increasingly studied for bioproduction and investigated for its novel applications. Recently, several prodigiosin-related reviews were reported. These studies covered some aspects of the general physicochemical properties, pathway synthesis, production, and applications of prodigiosin in medicine. However, only a few works discussed the eco-friendly production of prodigiosin from organic wastes. Remarkably, the scaling-up of prodigiosin production and its potential applications in agriculture have rarely been reviewed or discussed. This review extensively presents and discusses the green biosynthesis, enhancement, and scaling-up of prodigiosin production from a wide range of organic byproducts/wastes using different methods of fermentation. Notably, this paper highlights the novel and promising applications of prodigiosin in agriculture via in vitro tests, greenhouse tests, and field studies. The action mechanisms related to some potential bioactivities and the toxicology studies of prodigiosin are also discussed. This review thus supplies scientific data for further research and the application of prodigiosin in the future.