Enterprise architecture (EA) is a holistic approach that aligns IT resources with business processes and strategies. Thus, EA has been used in the public sector to improve services and service processes. How-ever, when EA programs are initiated, the organization faces several challenges, such as lack of re-sources or understanding, and radical changes in the organizational structures. In this paper, we study these problems in the public sector context and identify their root causes. We conduct a multiple-case study by deriving qualitative data from three provinces; each has different experiences, backgrounds, and skills. The findings highlight eight generic root causes and several public sector–specific problems. These findings help researchers and practitioners understand and promote EA, and avoid as many chal-lenges as possible as the root causes are known.