Plant factories with artificial lighting (PFALs), with an almost airtight and well-insulated structure, enable simple and accurate data acquisition and environmental control, time series analysis, and prediction related to plant phenotypes. With plant phenotyping based on cohort research in PFALs, the life cycle phenome history of both plant individuals and communities can be obtained non-invasively and continuously and analyzed from seed sowing to harvesting, with time series data on the microenvironment, management, and resource inputs/outputs. This chapter first reviews challenges affecting PFALs and introduces plant phenotyping in general, along with previous plant phenotyping studies in PFALs. Plant phenotyping based on plant cohort research in PFALs is also discussed, followed by experimental cohort research studies on individual phenotyping. Finally, the possibility of plant phenotype-based environmental control in PFALs, considering business-related factors, is discussed.