The highest share of the global population lives in cities. The current configuration of the latter requires considerable amounts of resource flows causing the degradation of local and global ecosystems. To face the complexity of these challenges, scientists use the concept of urban metabolism (UM), i.e. measuring urban input and output flows from a systemic perspective. This accounting method results in a large data collection from multiple sources that are often not harmonised. Metabolism of Cities Data Hub is an online platform which facilitates data collection, processing and visualisation in order to extract urban metabolism insights. This work highlights the challenges faced when mining urban metabolism data in the case of Lausanne and Geneva, as well as provides insights on how data could be best used from users and providers. Slight differences between the two case studies, in terms of data accessibility and availability where experienced but the main challenges revolved around data copyright, format and availability. As a conclusion, the used tool can enable harmonisation and standardisation of UM data. As such it could contribute to the use of data mining to streamline the environmental monitoring of cities as well as facilitate the creation of mitigation strategies.