We sought to establish a collaborative learning environment for our first-year university cell biology course that would be sufficiently challenging to warrant team effort and turn students into autonomous learners. We chose team-based science-writing blogs, a choice grounded in the Self Determination Theory. This theory posits that a sense of autonomy, competence and relatedness are essential requirements to perform a task in an autonomous-motivated fashion. Through surveys over a period of four years, we assessed how students perceived the blog project. Qualitative analyses revealed that students recognized and appreciated their autonomy. They also consistently considered as positive a sense of competence, expressed as being useful, and relatedness, i.e. relating with others and working together. A quantitative analysis based on an intrinsic-motivation inventory revealed that students experienced science-writing on the web as an intrinsically motivating learning task. We conclude that web-based learning triggers motivation to learn autonomously and discuss how task authenticity may play an important role in this process.