The aim of this multiple-case study was to research the key characteristics of project-based learning (PBL) and how teachers implement them within the context of science education. K-12 science teachers and their students’ videos, learning diaries and online questionnaire answers about their biology related PBL units, within the theme nature and environment, were analysed using deductive and inductive content analysis (n = 12 schools). The studied teachers are actively engaged in PBL as the schools had participated voluntarily in the international StarT programme of LUMA Centre Finland. The results indicate that PBL may specifically promote the use of collaboration, artefacts, technological tools, problem-centredness, and certain scientific practices, such as carrying out research, presenting results, and reflection within science education. However, it appeared that driving questions, learning goals set by students, students’ questions, the integrity of the project activities, and using the projects as a means to learn central content, may be more challenging to implement. Furthermore, although scientific practices had a strong role in the projects, it could not be defined how strongly student-led the inquiries were. The study also indicated that students and teachers may pay attention to different aspects of learning that happen through PBL. The results contribute towards a deeper understanding of the possibilities and challenges related to implementation of PBL and using scientific practices in classrooms. Furthermore, the results and the constructed framework of key characteristics can be useful in promoting research-based implementation and design of PBL science education, and in teacher training related to it.