Transplantation of stem cells, such as mesenchymal stem cells (MSCs), is a promising strategy for treating several types of intractable disorders. Mechanistically, it could not only replace damaged cells by direct contribution, but also establish an anti-inflammatory or immunomodulatory microenvironment. However, the cellular mechanisms underlying molecular and biological properties of stem cells during ex vivo expansion and also after transplantation in pathological environments remain largely elusive. We recently developed the cyanoacrylamide-based coumarin derivatives (Fluorescent real-time thiol tracer; FreSHtracer*) reversibly react with glutathione for monitoring of glutathione levels in living stem cells. These probes revealed that glutathione levels are heterogeneous among subcellular organelles and among individual cells and show dynamic changes and heterogeneity in repopulating stem cells depending on oxidative-stress or culture conditions. Importantly, a subpopulation of stem cells with high-glutathione levels exhibited increased self-renewal and migration activities in vitro and showed improved therapeutic efficiency in treating asthma. Furthermore, employing a novel combination of longitudinal intravital confocal fluorescence imaging and microcystoscopy in living animals, we investigated the distributions and properties of transplanted multipotent MSCs derived from human embryonic stem cells at single-cell resolution in real-time by performing confocal imaging of bladder tissues in a rat model of IC/BPS for up to 6 months post-transplantation. These novel real-time monitoring strategies demonstrate the novel molecular insight for maintaining stem cell functions and also enhance understanding of the in vivo behaviors of the engrafted stem cells, which is crucial to determine the efficacy and safety of stem cell-based therapies. This strategy may facilitate the translation of various stem cell-based approaches into clinical practice.