This paper examines the enterprise architecture process from the perspective of information systems controls, which refer to attempts to influence the behavior of employees in order to achieve organizational goals. Although controls have been extensively studied in processes such as systems development, there is little research examining control within the enterprise architecture process, despite its rising importance in today's organizations. This paper examines how enterprise architecture controls are employed in practice and considers the challenges faced in their design and operation. Drawing on empirical data from two in-depth case studies, enterprise architecture controls are classified and analyzed using COBIT 5. Our findings identify a series of specific challenges with enterprise architecture controls. Based on these challenges, we outline recommendations to practitioners in overseeing the enterprise architecture process and develop propositions to help guide future research initiatives to enhance enterprise architecture performance.