Approaches that are transdisciplinary and participatory can help to address complex socio-ecological issues by integrating multiple disciplinary perspectives while taking into account the different needs and experiences of community members and other stakeholders. Despite this promise, such approaches are rarely applied within the scientific community, as researchers and public actors often lack the training, practice and reference cases required to handle the working relationships and translations of terminology, ideas and values across multiple bodies of knowledge. A case study described in this manuscript depicts a group of researchers, artists and citizens consciously engaged in the construction of a transdisciplinary process as part of a 40-day ‘citizen science’ experiment focussed on assessing soil fertility in the urban area of Milan, Italy. The group drew from recognised scientific approaches, applied agronomic methodologies, artistic practices and technological tools, integrating them into a hybrid process of collective and participatory inquiry. As a quantitative outcome of the experiment, a dataset of bio-chemical parameters was generated, which was enriched by agronomic interpretations but also by artistic and reflective materials. Importantly, the process developed transdisciplinary and participatory skills, as it created a potentially replicable procedure of engagement, analysis and presentation for use in other citizen science settings. This article presents the context, the multiple objectives of the research and the applied approach and its timeline. Described in detail are the process of designing and conducting the experiment by involving an extended research community—including both junior and senior researchers—in progressive steps. Quantitative and qualitative results are provided. The findings are meant to contribute case material and methods to inform the advancement of transdisciplinary research approaches within the scientific community as well as examples of ways to transcend the boundaries of science to include artists and community stakeholders. The aspiration is to inform and inspire concrete application of transdisciplinary and participatory methods in concert to address complex socio-environmental challenges.