Stem cell-derived therapies have shown substantial promise in regenerative medicine for the treatment of degenerative diseases and injuries. Mesenchymal Stem Cells (MSCs) exhibit a remarkable capacity to differentiate into diverse cell types, modulate immune responses, and facilitate tissue repair. Nevertheless, concerns regarding their potential to induce tumors arise from their intrinsic properties, environmental factors, and genetic mutations that occur during handling. This review explores the intricate challenges associated with the tumorigenic potential of stem cell-derived therapeutic products and examines the underlying mechanisms contributing to this risk, such as oncogene activation, suppression of tumor suppressor genes, and the influence of the microenvironment on stem cell behavior. Furthermore, it delves into the role of epigenetic modifications and chromosomal aberrations in cell culture and expansion. This article provides an overview of strategies to mitigate tumorigenic risks, encompassing rigorous quality control measures, refined differentiation protocols, and advanced screening techniques. It also highlights innovative approaches, such as gene editing technologies and small-molecule modulation of stem cell behavior, as promising avenues to enhance safety. Despite these challenges, ongoing research and technological advancements are actively addressing these concerns to ensure safer and more effective utilization of stem cell-based therapies in clinical settings.