Higher Education Institutions (HEIs) face significant challenges in managing and integrating diverse Information System (ISs) that support academic, administrative, and strategic operations. As digital transformation advances, the need for seamless interoperability and data-driven governance becomes increasingly crucial. This study provides a comprehensive analysis of the ISs Ecosystem (ISE) in HEIs, emphasizing the importance of system integration, Business Intelligence (BI) solutions, and Decision Support Systems (DSS) in fostering efficient, data-driven decision-making. By examining a real-world case study of the University of Trás-os-Montes and Alto Douro (UTAD), this research validates the role of BI in transforming fragmented information landscapes into cohesive digital environments. The findings demonstrate that successful BI adoption requires well-defined governance structures, seamless data flow, and alignment with institutional objectives. Additionally, the study underscores the strategic impact of interoperability, highlighting how institutions can enhance institutional intelligence, streamline decision-making processes, and improve operational efficiency through an integrated BI ecosystem. The insights contribute to ongoing discussions on digital transformation in higher education, offering a scalable framework for HEIs seeking to transition from isolated systems to an interoperable and intelligent data ecosystem. The paper also explores emerging trends such as AI-driven analytics and predictive modelling, outlining potential pathways for HEIs to further optimize their decision-support infrastructures.