The fruit production industry is an important sector globally due to its nutritional, dietary, and economic value. Due to its significance as a crucial source of high-value, nutritious food, global demand for fruits has continuously risen over the years. However, fruit production is challenged by various factors, including biotic constraints or diseases caused by plant viruses. Diseases of fruit crops caused by plant viruses are difficult to manage because they are systemic once established and can easily spread via infected plant propagation materials. Thus, preventive measures are necessary to address the long-term impacts of plant virus diseases on fruit production. To manage the spread of plant viruses and ensure the propagation of virus-free fruit materials, international organizations, national governments, and other relevant stakeholders have formulated and implemented plant quarantine and certification programs. This chapter discusses the importance of virus disease management in fruit propagation through quarantine and certification programs. It highlights the certification programs implemented by major fruit-producing countries and outlines the challenges in implementing and future directions for fruit propagation quarantine and certification.