Abstract Industry 4.0 has ushered in a new era of digital manufacturing and in this context, digital twins are considered as the next wave of simulation technologies. The development and commissioning of Cyber Physical Systems (CPS) is taking advantage of these technologies to improve product quality while reducing costs and time to market. However, existing practices of virtual design prototyping and commissioning require the cooperation of domain specific engineering fields. This involves considerable effort as development is mostly carried out in different departments using vendor specific simulation tools. There is still no integrated simulation environment commercially available, in which all engineering disciplines can work collaboratively. This presents a major challenge when interlinking virtual models with their physical counterparts. This paper therefore addresses these challenges by implementing a holistic and vendor agnostic digital twin solution for design prototyping and commissioning practices. The solution was tested in an industrial use case, in which the digital twin effectively prototyped cost‐efficient solar assembly lines.