Many organizations have embraced agile methods. Studies show a trend of large-scale application of agile frameworks company-wide. Emergent architecture design as part of an agile approach is effective at the project level but causes issues when services need to interact seamlessly at the enterprise level. Enterprise architecture (EA) can provide such coherence. Combining the scaling agile methods with EA is challenging. However, such a combination could benefit from the flexibility that agile approaches offer and provide the consistency and long-term focus that EA pursues. This article uses the longitudinal case study research to explore how organizations can effectively govern Agile and EA in large-scale agile transformations. Our case analysis shows that methods for scaling Agile do not provide sufficient guidance to properly handle the transformation from existing EA practices to an Agile EA combination company-wide. We propose how EA can be applied effectively in large-scale agile transformations despite the two seemingly conflicting approaches of Agile and EA. Based on our findings, we propose a conceptual model for future research that incorporates factors that take EA into account in the governance of agile-scaling frameworks. Our findings extend current literature on coordination mechanisms between architects and agile teams in large-scale agile transformations, thereby balancing emergent and intentional architectures.