The period of adolescence brings with it a dynamic interaction between social context and behaviour, structural brain development, and anxiety and depressive symptoms. The rate of volumetric change in the ventromedial prefrontal cortex (vmPFC) and amygdala have been implicated in socioemotional development in adolescence; typically, there is thinning of grey matter volume (GMV) in the vmPFC and growth in the amygdala during this time. The directionality of the associations between social, emotional, and neuroanatomical factors has yet to be untangled, such as the degree to which social variables impact regional brain development, and vice versa. To add, the differences between sexes are still up for debate. In this study, longitudinal associations between peer problems, family support, socioeconomic stress, emotional symptoms, amygdala volume, and vmPFC GMV were investigated for both sexes using latent change score models. Data from a multi-site European study at baseline (mean (SD) age = 14.40 (0.38) years; % female = 53.19) and follow-up 2 (mean (SD) age = 18.90 (0.69) years, % female = 53.19) were used. Results revealed that peer problems did not predict emotional symptoms, rather they changed together over time. For males only, there was positive correlated change between vmPFC GMV, peer problems and emotional symptoms, indicating that slower vmPFC GMV thinning was associated with poorer social and emotional functioning. Additionally, greater family support at age 14 years was associated with slower growth of amygdala volume between ages 14 and 19 years for males; previous research has related slower amygdala growth to resilience to mental health disorders. The findings have extended understanding of mutual social, emotional and brain development, and avenues to protect mental health.