The capstone project (CP) process is an essential layer on the path towards an engineering degree. Typically, the purpose of the CP is to build an actual product prototype. In practice, the process of guiding the CP is less structured than a standard course. This is due to the project's scope and span, the interaction between the student and the academic supervisor and the exogenous workload of the student. The CP process thus requires the academic system to provide a combination of creative, professional guidance and, at the same time, strict management of the process. This paper outlines a methodical way to conduct this complex and challenging process, which we have adopted and refined in the last three years and shares some observations we have made during this period. The essence is the separation between the content and procedural aspects of the project. This contrasts with how CPs were previously managed, where the guiding academic staff were responsible for both aspects. This separation standardizes and optimizes the process and is carried out parallel to the execution of the projects. The main change in the curriculum is the addition of two dedicated courses spanning the last three semesters of studies called “CP Seminar 1” and “CP Seminar 2”. These seminar courses are guided by a team of two professors, who meet with students every two weeks, working toward well-defined and structured milestones. During the courses, students develop an understanding of the conception, design, implementation, and operation of the product they develop as their CP. Thus, greater control, and monitoring of the progress of the students in the process is achieved by the supervisors, the seminar team, and the students themselves. The courses frame the CP process and facilitate strict milestones, standardized documentation, and substantial validation.