In batch plants, as we attempt to increase annual throughput, we run into bottlenecks that are either equipment or resource (e.g. utilities, labor) related. Throughput bottlenecks are equipment or resources that limit the amount of product produced per batch. Scheduling bottlenecks are units or resources that limit the number of batches that can be processed per year or campaign. In this payer, we present a systematic simulation-based methodology for identifying bottlenecks in batch processing and a strategy for eliminating them. The decision-making process is based on a set of operation-related variables that are used to indicate the presence of bottlenecks. The implementation of the methodology is demonstrated with the use of a synthetic pharmaceutical example.