By bringing various technological advances together, Industry 4.0 promises production systems to boost in productivity. The transformation of the existing production systems into an Industry 4.0 factory is a strategic and long-term undertaking which needs a high capital investment, training of personnel and change of the environment and the culture in almost all of the functions of the value chain. Thus, it is required to be planned well by the companies. To be successful in the Industry 4.0 era, companies will not only have to simultaneously execute interdependent projects, but also require to perform project portfolio selection task in multi-dimensional environments in the presence of high uncertainty. Since determining optimal project portfolio for digital transformation among various project alternatives demands the consideration of multiple constraints and interdependencies, an integer programming model is proposed to address this problem in this chapter. To demonstrate its effectiveness and practicality, the proposed optimization model is applied to the Industry 4.0 project alternatives of an automotive manufacturer.