Ontology-based data access (OBDA) is a novel paradigm for accessing large data repositories through an ontology, that is a formal description of a domain of interest. Supporting the management of OBDA applications poses new challenges, as it requires to provide effective tools for (i) allowing both expert and non-expert users to analyze the OBDA specification, (ii) collaboratively documenting the ontology, (iii) exploiting OBDA services, such as query answering and automated reasoning over ontologies, e.g., to support data quality check, and (iv) tuning the OBDA application towards optimized performances. To fulfill these challenges, we have built a novel system, called MASTRO STUDIO, based on a tool for automated reasoning over ontologies, enhanced with a suite of tools and optimization facilities for managing OBDA applications. To show the effectiveness of MASTRO STUDIO, we demonstrate its usage in one OBDA application developed in collaboration with the Italian Ministry of Economy and Finance.