Physical activity (PA) strongly decreases when children make the transition from primary to secondary school. The study aimed to investigate how individual and social environmental factors toward PA changed when children (11-12years) made the transition from primary to secondary school (13-14years) and how changes in these factors were related to changes in different PA domains. In total, 321 children (48.9% girls) and one of their parents both filled out a questionnaire concerning individual (i.e., attitude, self-efficacy, perceived benefits, and barriers of PA) and social environmental factors related to PA (parental support, friend's co-participation, parental trust in child's ability to be physically active, and social norm) in the last grade of primary school and 2years later. Children wore an activity monitor for 7days and self-reported different domains of PA. Most individual and social factors became less positive toward PA after the transition to secondary school. Among girls, a more positive attitude and an increase in self-efficacy were related to an increase in average daily steps and sports during leisure, respectively. Among boys, a decrease in perceived barriers (lack of time and parental reported lack of transportation to sport activities) was related to a decrease in average daily steps. An increase in parental support and a decrease in the parental perceived barrier of not liking sports were related to an increase in sports during leisure. The prevention of adverse changes in individual and social factors toward physical activity may lead to a smaller decrease or an increase in physical activity.