Adolescents at risk and living in deprived areas have fewer opportunities for out of school activities, informal learning and reduced access to science education. In addition, teenagers seem to have, in general, a lack of interest in Science. Besides, research showed how the social determinants of health, and specifically, deprivation and lower access to health information, have major consequences in terms of chronic diseases. Scientific literacy can be promoted through enhancing health education: health research is well-valued in the society; topics are practical and relevant, and it is important to change unhealthy habits as early as possible; self-leadership and active methods would be key ingredients. There is a need for evidence and validation of effective interventions for fostering science education and public participation with teenagers and young adults from vulnerable and/or deprived populations to raise their academic outputs, while contributing to improve empowerment in health for this group. SEEDS aims at fostering science literacy and STEM education by raising the health understanding, also pursuing the empowerment of youth in critical thinking skills, self-management and self-care through community-based public engagement, therefore improving effectiveness of health promotion interventions in this population. The multi-stakeholder participatory intervention merges the dialogue between citizen science and traditional science. SEEDS joins together the key players in science and society by applying the 4Helix model of stakeholders. Teenagers lead the process; the scientific literacy will be accompanied by a depth health education able to transform their habits, contributing to sustainable behavioural change.