Problem-based learning (PBL) is an acclaimed educational concept for laboratory teaching in chemistry, which significantly affects learner motivation. A central aim of PBL is to overcome educational problems with "cook-book" laboratories. For example, when students receive experimental instructions and apply the instructions similar to recipes, they do not necessarily understand what they do and why. However, research in problem-based laboratories still produces inconsistent and even contrasting results. A reason for this is the research focus; the problem-based concept and the outcome (e.g., learning results) are often investigated without considering the implementation of the problem. According to self-determination theory (SDT), it is necessary for problem-based learning to invoke a sense of autonomy, competence, and relatedness in the students to foster intrinsic learner motivation. To understand better the mechanisms and potential of PBL in enhancing intrinsic motivation, it is pivotal to investigate and identify connections to the practical implementation. This study focuses on intrinsic motivation connected to implementation. The aim was to clarify central implementation strategies for PBL concepts that enhance intrinsic learner motivation. To this end, we conducted semistructured interviews with undergraduate, nonmajor chemistry students who attended an innovative, industry-based PBL-laboratory course and analyzed them using qualitative content analysis. The results suggest central implementation factors that are interconnected and led to a novel model of the autonomous scientific process. The factors that enhance intrinsic motivation in this model are the independent acquisition of information, the design and application of the experimental procedure, the gathering of feedback through experiments, and the possibility to optimize the process. Adequate strategies must be taught to the students to enable autonomy and are exemplified in this study. The students perceived the presented industry-based problem setup as an authentic, autonomous scientific process, thus appealing to their self-perception as scientists.