In order to lead successful projects, coordinating the different business units of a company is compulsory. This paper proposes a framework to make companies’ practices evolve toward a better alignment of the business units based on their processes, and illustrates it with project management and systems engineering processes. Indeed, all the different organization units intend to serve the common global objective to satisfy the customer needs, and need to closely collaborate during projects. However, work organization in companies often leads to barriers between these stakeholders, with the result of an incoherent decision-making that may compromise project execution. Therefore, the issue of processes alignment from different domains lies at the very heart of ongoing research topics and ranks first among economic and industrial concerns. This paper uses a qualitative approach to show how different business units’ processes can be integrated and illustrate this framework by aligning the systems engineering and project management processes within a certain engineering project context. By using the proposed framework, different teams (or even different companies, in a context of distributed enterprise) can align their practices, while also making them evolve toward a better compliance with standards.