ABSTRACT Bottleneck detection and management plays a significant role in the context of Industry 4.0, wherein process chains have become more intricate. The dynamic nature of process chains shifts the bottleneck location, which requires an integrated methodology capable of identifying current as well as predicting future bottlenecks. The paper proposes a cognitive digital twin (CDT) with a novel explainable artificial intelligence (XAI) model. The proposed CDT is capable of (i) detecting existing bottlenecks, (ii) detecting data anomalies and process chain anomalies (iii) estimating shifting bottlenecks due to anomalies, (iv) predicting near future bottlenecks, and (v) the XAI model supports operational and strategic decision making. The usefulness of proposed CDT is demonstrated and validated experimentally on an industry 4.0 compliant learning factory. The proposed novel CDT effectively addresses the process chain bottlenecks (existing, shifting, and future) while the XAI model enhances transparency and trustworthiness for practical implementation.