Social and economic changes occurring in the last two decades in Mozambique may have induced lifestyle changes among youth. This study aimed to document secular changes in habitual physical activities of Mozambican youth between 1992, 1999 and 2012. A total of 3393 youth (eight–15 years), were measured in three different time periods (1992, 1999, 2012). Habitual physical activity (PA) was estimated with a questionnaire, including items related to household chores, sport participation, traditional games and walking activities. Biological maturation was assessed. Analysis of Covariance (ANCOVA) was used to compare mean differences in PA across the years. Significant decreases between 1992–1999 and 1992–2012 were observed for boys in household chores, games and walking, and a significant decline between 1999 and 2012 was found in sport participation.Among girls, a significant and consistent decline (1992 > 1999 > 2012) was observed for household chores, a decline between 1992–1999 and 1992–2012 for games and walking, and a significant increase between 1992 and 1999 in sport participation. In general, a negative secular trend was found in habitual PA among Mozambican youth. Interventions aimed at increasing PA represent important educational and public health opportunities.