Effectiveness of school-based physical activity (PA) initiatives is not only measured by short term impact on PA levels, but on modifiable determinants of PA such as perceptions and motivations towards PA engagement. These determinants predict more long-term effects and, when it comes to PA promotion, are potentially influenced not only by "what we do" but "the way that we do it". "The Active School Flag" is a whole school process-oriented physical activity initiative that aims to get more schools, more active, more often. In this exploratory study, a mixed methods research approach is taken to examine the differential impact of the Active School Flag compared to the outcome-oriented PA initiative "The Daily Mile" on measured PA and perceptions of PA, in Irish primary school children. Accelerometry data (n = 124; 41% girls) and focus group data (n = 24; 50% girls) were collected from four schools of low socioeconomic status at baseline and follow up (eight months later). Two schools implemented the Active School Flag initiative and two implemented the Daily Mile initiative. Contrasting trajectories in PA levels were observed over time with Daily Mile participants demonstrating a significant decrease in PA levels from baseline to follow up (P = 0.004), and Active School Flag participants demonstrating a significant increase (P < 0.001) over the same timeframe. This meant that while Daily Mile participants had significantly higher levels of PA at baseline compared to Active School Flag participants (P < 0.001), Active School Flag participants experienced a positive trajectory which saw them to "catch up" to TDM participants by follow up. From a qualitative perspective, 4 key themes, 1) Affordance of choice, 2) An appropriate level of challenge, 3) Importance of social interactions and 4