The Problem Based Learning (PBL) as student centred approach and learning-by-doing method is suited for the modern higher education. However, the first contact with the method can be overwhelming for the students, in the absence of prior domain knowledge. The preparation of the learning material can be time and resource consuming for the teacher. The goal of the research was the implementation of an environment that should enhance the learning experience for the student and reduce the implementation burden for the teacher. The environment is based on the ADOxx platform and allows the collaboration of the learner teams and the teacher-learner interaction on three levels. The Metamodeling level supports the development of the domain-specific language used in the modelling of the manufacturing system; this activity stimulates and directs the gathering and consolidation of domain-specific knowledge. The modelling level allows the development of alternative design solution using models of the factory components. The Simulation level allows the analysis of these variants. The environment supports the teacher in developing instructional scaffolding and uses cases to ease the learners the first time contact with PBL. The functionality of the environment is presented using the case of designing a flexible food production line.