First-year university is a time of significant adjustment for students, and the experience of academic stress is common, with tertiary institutions seeking to understand these experiences in order to better support students through this time. Protective behaviours, such as engagement in mindfulness via interventions, are known to improve psychological well-being and can reduce the experience of academic stress. Recent literature suggests that there may be a reciprocal relationship, given that perceived stress may also be a contextual factor associated with the likelihood of expressing mindful tendencies. However, limited research has investigated the relationship between the fluctuating expression of mindful tendencies and perceived academic stress in a natural university setting. The first aim of the present longitudinal weekly diary study was to explore co-occurring fluctuations in weekly mindfulness engagement and perceived university-related stress, to establish a reciprocal longitudinal predictive relationship. The study also aimed to establish whether this reciprocal relationship could predict future psychological well-being. During first semester 2020, first-year university students (N = 69) completed a series of weekly diaries for nine weeks during the university semester, reporting their expression of mindful tendencies and perceived university-related stress. Psychological well-being was measured in the final week of semester. Results supported the reciprocal predictive relationship: The expression of mindful tendencies one week significantly independently predicted lower perceived stress the following week, and similarly higher perceived stress significantly independently predicted subsequent lower mindfulness. Results also revealed that mindfulness indirectly predicted psychological well-being via the subsequent week’s perceived stress. The results provide strong support for a cycle of mindfulness and perceived stress that is ultimately important for predicting future psychological well-being. This provides insight into the potential benefit of simple mindfulness-based interventions to support university students, especially during the transition into tertiary studies. These results have important implications for mindfulness-based interventions, and demonstrate the benefit of using more complex methodologies to understand the natural experience of university students.