Managing and dealing with variability in business processes and the IT landscape is a common challenge in the everyday practice of most enterprises and organizations. Recent studies have observed that digital transformation, Internet-of-Things solutions and the introduction of artificial intelligence cause changes and challenges in enterprises that simultaneously require variability on several levels, for instance, business processes, data architecture, and services. Enterprise architecture models are considered a suitable way to visualize and manage dependencies between different levels of an enterprise. However, the management of variability in enterprise architectures has not received much attention in scientific research. This article† aims to contribute to a better understanding of future investigation needs. Using a systematic literature analysis, the article structures the existing research work in the field and examines real-world challenges of variability based on a case study. We argue that there is a need for new constructs in enterprise architecture models that allow for expressing dependencies between variations on different enterprise architecture layers.