Objectives Intervention participants' responses to and engagement with interventions are a key intermediate step between interventions and intended outcomes. The aim of this study was to qualitatively investigate crucial aspects of engagement, namely acceptability (experienced cognitive and emotional responses to the intervention), receipt (comprehension of intervention content), and skill enactment (skill performance in target settings), within the Let's Move It, a multi-component school-based physical activity intervention. Design A longitudinal qualitative study embedded in a cluster-randomized trial, with individual interviews of purposefully sampled intervention participants immediately post-intervention (n = 21) and at 14 months (n = 14). Methods Semi-structured interviews were analysed using thematic analysis. Abductive coding process was taken to identify categories for themes. Results The analysis resulted in 12 themes and 18 subthemes. Overall, participants reported perceived effectiveness of and affective attitude towards the intervention (acceptability) and understood the main messages and skills (receipt). For example, findings indicated comprehension of the non-judgemental nature and choice-providing messages of the intervention underpinned by self-determination theory. Despite reporting understanding how and why to perform the skills, not using them was a highlighted theme (skill enactment), particularly for self-regulatory techniques such as planning. Friends' role as key self-motivation technique was a prevalent theme. In the within-individual analysis, three different engager types were identified: positive, ambivalent, and negative. Conclusion Identifying misunderstandings and difficulties in skill acquisition can help interpret main trial outcomes and inform further intervention optimization. This study provides an example of how to use thematic analysis to assess acceptability, receipt, and enactment in interventions.