Few studies have examined the effects of early-life nutrition interventions on adolescent physical activity (PA). We aimed to examine the long-term effects of small-quantity lipid-based nutrient supplements (SQ-LNS) on adolescent PA and sedentary behaviour (SB) and to describe current adolescent PA and SB levels in this cohort. In the International Lipid-Based Nutrient Supplements (iLiNS)-DYAD-Ghana trial, 1320 mothers were enrolled and randomly assigned to one of three conditions: (1) daily iron and folic acid during pregnancy and placebo (calcium) from birth to 6 months postpartum (IFA), (2) multiple micronutrient supplements during pregnancy to 6 months postpartum (MMN) or (3) SQ-LNS during pregnancy to 6 months postpartum (LNS). Infants from mothers in the LNS group received SQ-LNS designed for children from 6 to 18 months. We recruited 11–13-year-old adolescents of mothers enrolled in the iLiNS-DYAD-G trial for a 7-d PA and SB assessment using accelerometers (n 305) and self-reported PA and SB (n 508). We compared the LNS with non-LNS (IFA+MMN) groups using ANCOVA models for the following outcomes: mean vector magnitude counts per minute, PAQ-C score and percentage of time in SB, light PA and moderate-to-vigorous PA (MVPA). There were no significant differences between the LNS and non-LNS groups in any PA outcome in minimally or fully adjusted models. Only approximately 50 % of adolescents met the PA recommendation of 60 min/d MVPA, with males more active than females; however, there is room for improvement. SQ-LNS in early life does not appear to have a sustained impact on PA or SB.