Background The role of physical activity (PA) in minimizing non-communicable diseases is well established. Measurement bias can be reduced via ecological momentary assessments (EMAs) deployed via citizen-owned smartphones. This study aims to engage citizen scientists to understand how PA reported digitally by retrospective and prospective measures varies within the same cohort. Methods This study used the digital citizen science approach to collaborate with citizen scientists, aged 13-21 years over eight consecutive days via a custom-built app. Citizen scientists were recruited through schools in Regina, Saskatchewan, Canada in 2018 (August 31 - December 31). Retrospective PA was assessed through a survey, which was adapted from three validated PA surveys to suit smartphone-based data collection, and prospective PA was assessed through time-triggered EMAs deployed consecutively every day, from day 1 to day 8, including weekdays and weekends. Data analyses included t-test to understand the difference in PA reported retrospectively and prospectively, and linear regressions to assess contextual and demographic factors associated with PA reported retrospectively and prospectively. Result Findings showed a significant difference between PA reported retrospectively and prospectively (p = 0.001). Ethnicity (visible minorities: β = - 0.911, 95% C.I.= -1.677, -0.146), parental education (university: β = 0.978, 95% C.I.= 0.308, 1.649), and strength training (at least one day: β = 0.932, 95% C.I.= 0.108, 1.755) were associated with PA reported prospectively. In contrast, the number of active friends (at least one friend: β = 0.741, 95% C.I.= 0.026, 1.458) was associated with retrospective PA. Conclusion Physical inactivity is the fourth leading cause of mortality globally, which requires accurate monitoring to inform population health interventions. In this digital age, where ubiquitous devices provide real-time engagement capabilities, digital citizen science can transform how we measure behaviours using citizen-owned ubiquitous digital tools to support prevention and treatment of non-communicable diseases.