Magalhães was raised in , the capital of what is now the municipality of Bobonaro in the west of East Timor. He is the second child of Manuel Magalhães and Regina Cardoso Gouveia Leite, who had five daughters and three other sons, including the PD politician , State Secretary for Youth and Labor from 2017 to 2018. Manuel Magalhães was killed during the 1999 East Timorese crisis.