This paper explains the steps carried out for the design of an educational innovation and the outcomes of its implementation. The innovation consists of integrating the contents of two courses (‘biological wastewater treatment’ and ‘bioprocesses applied to the treatment of wastes’) for the same academic year using project-based learning methodology to connect knowledge between subjects and to utilize transversal competences. Students from the second year of a chemical engineering master’s degree worked on an open-ended project based on a current environmental problem. This methodology lets the students properly acquire several transversal competences, such as ‘Design and project’, ‘Teamwork and leadership’, and ‘Effective communication’, which were evaluated with rubrics. However, according to the students’ perception, other skills, such as ‘Comprehension and integration, analysis and problem solving’, ‘Knowledge of contemporary problems’, and ‘Planning and time management’, were also worked on and improved. Based on the results from the matrix analysis and the Likert questionnaire, the organization and development of the activity were positively assessed, highlighting the importance of the lecturers’ feedback. The learning outcome in terms of knowledge integration was accomplished, reaching project marks 8.5–10 on a 0–10 scale.