Research-based blended learning (RBBL) allows students to be part of an authentic scientific discovery process. In this study, students' perception and motivation of the RBBL coupled with Scrum methodology in a third-year polytechnic chemistry laboratory course were investigated. Results showed that the scaffolded approach, designed referencing the Community of Inquiry (CoI) framework and learning presence, developed students' technical and process skills (adaptability, critical thinking, and problem solving skills). With the positive student-instructor interaction experienced by the students, they were confident, engaged, and motivated to work on the research project despite its complexity.