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After the progressively disruptive adoption of co-design methods for the conceptualisation and definition of diverse types of projects outside Academy and the sciences, its appropriation for dynamising teamwork and collectively generating knowledge is applicable, useful and advantageous in different types of collaborative research projects. Based on the analysis of three embedded case studies, this paper explores the adoption of design thinking for the co-creation of citizen science experiments. Citizen science, as a paradigmatic field of collaborative research, can benefit significantly from co-design techniques, evolving from a ‘contributory’ to a ‘co-created’ model. The results presented derive from a project involving a scientific team and a co-creation facilitator with different groups of secondary students, from three schools in different socio-demographic contexts around Barcelona. Based on the first version of a ‘Collaborative Research Toolkit’, participants developed through a series of sessions and iterations preliminary designs of experiments about human behaviour, moving from the initial identification of shared concerns to several “mockup” versions of research sequences and methods. Specific steps of the co-creation process involved discussions about social impact, feasibility and motivation around local issues, collaboratively defined research questions, and logistics needed for the management and production tasks behind each experiment realization. Based on data from participant observation, artifact analysis, semi-structured interviews and a participant’s survey, the study compares the process and outputs of these three citizen science co-design experiences, describing how some co-creation techniques can help or not to define collaborative research practices, specially for generating effective participative research ideation, design and planning. Further questions related to the co-design of collaborative research processes in other fields, like action research or team science, are also derived from this meta-research project.