Citizen science has grown as a promising way to promote scientific education and democracy. However, the realization of these goals has been hampered as most programs in educational and other settings have used top-down approaches (where scientists direct the whole research path). Here we present a school bottom-up initiative, where students’ interests are raised and collaborative projects are developed in academies formed by students, teachers and scientists. Projects addressing local territorial identities are especially motivated by the program. In this work, we explored: (i) diversity of interests, (ii) learning outcomes, and (iii) the scientific quality of the projects. In two years of implementation in the intercultural south of Chile, we have worked with 52 academies, in projects covering a variety of research topics, including some that seek to rescue Mapuche’s traditional knowledge. We have observed the promotion of scientific and socioemotional skills in students, and projects have been judged of high quality by independent panels of experts. These results support the feasibility of citizen science to promote learning and to foster links between school and scientific institutions towards a more democratic scientific development.