Plant cell culture is an effective technology for the production of valuable plant‐derived secondary metabolites which can be used as pharmaceuticals, food additives, nutraceuticals, etc. The biosynthesis of secondary metabolites by cell culture is safe, controllable, and economical in contrast to field cultivation of their parent plants; but it is also affected by many internal and external factors. In this chapter, the background of secondary product accumulation by plant cell culture is overviewed at first. The progress in recent years toward manipulation of environmental factors, bioprocessing strategies, and elicitation and signal transduction engineering are summarized with typical examples for each case. Furthermore, advances in modulation of secondary metabolite accumulation including heterogeneity engineering, metabolic engineering, and omics study of secondary metabolite biosynthesis, are also reviewed. Further developments in rational bioprocessing and in systems biotechnology of plant cells for metabolite production are expected in the future.