Regular physical activity and mindfulness training both have been shown to improve cognitive functioning among different populations, especially for older adults and children. These associations are less understood in young adults and at the momentary (i.e., within-person) level of analysis. This study examined relations among momentary levels of activity, mindfulness and cognitive functioning in university students under daily context. University students (N = 158) used a mobile phone application to provide 14,589 momentary self-reports (M = 92 reports/person) over two weeks. About 2/3 (62%) of the sampled moments were allocated in sedentary activities, whereas about 1/3 (38%) of the sampled moments were reported spent standing or moving. Approximately 40% of the variance in momentary cognitive functioning was attributed to between-person differences. At the within-person level, cognitive functioning was higher when moving (compared to sitting), and state mindfulness increased the association between momentary movement and cognitive function. At the between-person level, usual mindfulness was positively associated with cognitive functioning. There were no significant differences in usual levels of cognitive functioning by the day of week, or usual levels of standing or moving (compared to sitting). In sum, after controlling for usual and momentary stress, within-person associations were identified among momentary activity, mindfulness and cognitive functioning. These results inform how interventions might be designed to promote physical activity and enhance cognitive functioning for university students.