This article delves into the application of Virtual Commissioning (VC) using Digital Twin (DT) technology to optimize automated manufacturing systems. The research focuses on a vane scanning process within an industrial test environment. The main goal is to identify the challenges of integrating VC and DT into current manufacturing workflows, with a strong emphasis on early fault detection, optimizing systems, and efficient use of resources. This article provides a structured framework for VC, offering strategic information to make the VC implementation process easier and more efficient for industry practitioners. In addition to that, it significantly contributes to understanding VC’s potential to make manufacturing processes more efficient, lower operational costs, and improve overall system performance. A key outcome of this research was the successful validation of a virtual model, which played a crucial role in identifying essential factors for effective VC implementation. These factors include ensuring tool compatibility, maintaining interoperability, and integrating real-time data during the commissioning process. Furthermore, the findings are particularly valuable for advancing smart manufacturing practices and enhancing the deployment of automated systems as well as the importance of incorporating VC into the development and procurement of new automated manufacturing systems, providing a clear path to fully utilize the benefits of digital twin technology in industrial settings.