Data from automated fare collection systems have become almost essential in the study of the mobility of people using public transport. Among other advantages, the data collected enable longitudinal studies to be carried out with a detail that other sources cannot approximate. However, despite the great potential of these data, the data collecting systems are usually intended for purely accounting purposes and not for carrying out mobility studies. Largely for this reason, these data are not always used to their full potential, and so it is necessary to propose strategies that allow the preparation and exploitation of these data, especially in those cases where the usefulness and value of the data have not yet been proven. This study proposes a workflow that seeks to prevent duplication of efforts when querying this type of data. The implementation of a generic database model and a protocol for sharing meaningful queries and results greatly facilitates an initial analysis of these data. This strategy has been applied within a specific project, but it could be the basis for sharing methods between different studies.