In the last decade, smartphone users grown from 2.8 billion worldwide in 2018 to 3.8 billion in 2021. This fact associates with greater ease of publishing and accessing fake news. This is a particularly concerning issue in a global crisis situation such as the COVID-19 pandemic. As stated by the WHO, this is a global health crisis and the spread of fake information could have a direct impact on people’s wellbeing. Due to this situation, all systems which compose the quadruple helix (i.e., science, economy, politics and media and culture-based public) are under great pressure. On the one hand, citizens demand fast and trusted information, and on the other hand, the scientific community is pushed to publish, resulting in scientific papers published very fast and, sometimes, without adequate peer review processes, as reflected by the unprecedented number of retreats. The PandeVITA ecosystem will contribute to offering a better understanding of how societal actors’ behave, understanding their reaction to and interaction with science and health developments in the context of pandemics, with the aim to encourage citizens to contribute to scientific research with different kinds of data. This paper describes a novel approach to citizen science interventions and user engagement based on motivational theory and behavioral science, aiming to provide a set of architectural components, technologies, tools and analytics to assess citizens’ activities, system performance and stakeholders-related key performance indicators (KPIs) in an observatory fashion, allowing to investigate the motivation of the target participants, user engagement and long-term retention.