Digital Transformation has become a fundamental ally in addressing the constant demands faced by Higher Education Institutions (HEI), and it has also introduced complex scenarios that require adaptation in the implementation of business processes and supporting technologies. This research presents the findings of a case study at Politécnica Salesiana University (UPS by IT acronym in Spanish) of Ecuador where, through observations and interviews, the perception of experts in business process analysis and IT was reflected. The results regard the relationships and interdependencies between these two management areas, the tools employed to facilitate interaction, and the challenges present in complex and unpredictable scenarios within an HEI. Likewise, potential support mechanisms to tackle these scenarios are discussed. The results underscore the importance of analyzing the human factor to achieve alignment between Information Technology (IT) Management and Business Process Management.