Despite evidence for the utility of self-determination theory in physical education, few studies used objective indicators of physical activity and mapped out between-class, relative to between-student, differences in physical activity. This study investigated whether moderate-to-vigorous physical activity (MVPA) and rated collective engagement in physical education were associated with autonomous motivation, controlled motivation, and amotivation at the between-class and between-student levels. Participants were 739 pupils (46.3% boys, Mage = 14.36 ± 1.94) from 46 secondary school classes in Flanders (Belgium). Multilevel analyses indicated that 37% and 63% of the variance in MVPA was explained by between-student and between-class differences, respectively. Students’ personal autonomous motivation related positively to MVPA. Average autonomous class motivation was positively related to between-class variation in MVPA and collective engagement. Average controlled class motivation and average class amotivation were negatively associated with collective engagement. The findings are discussed in light of self-determination theory’s emphasis on quality of motivation.