Physical activity at school can be beneficial to children's psychosocial well-being. To realise this potential, a school environment that supports physical activity is crucial. Self-Determination Theory provides the basis for one approach, namely to focus on pupils' need to feel competent, autonomous and related. The purpose of this study was to investigate how pupils experienced a school physical activity intervention based on Self-Determination Theory and to assess whether the components developed for the intervention appeared to increase the pupils' sense of competence, autonomy and relatedness, thereby furthering their psychosocial well-being. Two schools were selected to take part in a qualitative case study, with one grade four (ages 9-10) and one grade six (ages 12-13) class selected for closer monitoring. Ten semi-structured focus group interviews were carried out, involving 36 pupils, combined with 28 days of participant observations. The data were analysed based on the principles of deductive content analysis, using competence, autonomy and relatedness in the categorisation matrix. Findings showed that the pupils' sense of relatedness was central to well-being and influenced their sense of competence and autonomy. Changing the physical activity climate to focus on mastery and learning instead of competing and performance was challenging, but in some instances brought about more positive experiences, especially for pupils with limited motivation in school physical activity. Finally, while being given influence and choice evidently promoted the sense of autonomy, some pupils felt uncomfortable choosing activities on behalf of the group.