Implementing a new laboratory information system (LIS) presents an opportunity to improve operational efficiency and streamline reporting by refining workflows by utilizing LIS functionality. Flow cytometry laboratories face unique challenges because the specimen and test results may be categorized under clinical pathology (CP), anatomic pathology (AP), or both. We describe the design and implementation of reporting flow cytometry results within the Epic Beaker CP module, its interface with the Epic Beaker AP module, and integrated reporting for AP/CP cases at an academic institution. This manuscript emphasizes the challenges and steps needed to integrate anatomic and clinical pathology workflows by leveraging LIS functionality to implement electronic and predominantly paperless workflows within a flow cytometry laboratory.