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Container terminal capacity is often limited by (in)efficiency bottlenecks. This paper provides the design and proof of concept for the bottleneck mitigation cycle (BMC), consisting of three steps: bottleneck classification, detection and alleviation. While, often, the literature only focuses on alleviation of a single bottleneck and ignores bottleneck detection and interdependencies, this research uses the shifting bottleneck method and thereby considers a variety of possible infrastructural and operational bottlenecks. An empirical approach is adopted to find the cause of the detected bottleneck and to suggest suitable alleviation measures. Application of the BMC to a simulation model of the Fergusson Container Terminal in the Port of Auckland resulted in productivity improvements of 2–6%. To further improve the BMC, future research directions are to improve the empirical approach used for bottleneck alleviation and to apply the BMC in real-time.