Medicinal plants play a vital role in healthcare and the pharmaceutical industry, yet they face growing threats from habitat degradation, overexploitation, and unsustainable practices. While cultivation and domestication can aid conservation and ensure a steady supply, these processes may also diminish genetic diversity and alter phytochemical compositions, potentially reducing adaptive traits found in wild populations. Conservation strategies, both in-situ and ex-situ—such as field gene banks, cryopreservation, and sustainable harvesting—combined with advances in molecular genetics and biotechnology, provide valuable tools for maintaining genetic resilience and metabolomic diversity. Integrating traditional conservation approaches with modern breeding and genomic technologies is essential to achieve a balance between sustainable use and biodiversity protection. This review summarizes the current understanding of how cultivation and domestication affect the genetic diversity and phytochemistry of medicinal plants, while also highlighting future directions for conservation, research, and policy development. Moreover, this research emphasizes the rich diversity of Turkey’s medicinal plants, details key approaches and conditions necessary for their sustainable utilization and conservation, and demonstrates their therapeutic value through selected examples.