BackgroundProton therapy is an effective treatment for ocular melanoma, and other tumors of the eye. The fixed horizontal beamline dedicated to ocular treatments at Massachusetts General Hospital was originally commissioned in 2002, with much of the equipment, safety features, and practices dating back to an earlier implementation at Harvard Cyclotron in the 1970s.PurposeTo describe the experience of reevaluation and enhancement of the safety environment for one of the longest continuously operating proton therapy programs.MethodsSeveral enhancements in quality control had been introduced throughout the years of operation, as described in this manuscript, to better align the practice with the evolving standards of proton therapy and the demands of a modern hospital. We spotlight the design and results of the failure mode and effect analysis (FMEA), and subsequent actions introduced to mitigate the modes associated with elevated risk. The findings of the FMEA informed the specifications for the new software application, which facilitated the improved management of the treatment workflow and the image‐guidance aspects of ocular treatments.ResultsEleven failure modes identified as having the highest risk are described. Six of these were mitigated with the clinical roll‐out of a new application for image‐guided radiation therapy (IGRT). Others were addressed through task automation, the broader introduction of checklists, and enhancements in pre‐treatment staff‐led time‐out.ConclusionsThroughout the task of modernizing the safety system of our dedicated ocular beamline, FMEA proved to be an effective instrument in soliciting inputs from the staff about safety and workflow concerns, helping to identify steps associated with elevated failure risks. Risks were reduced with the clinical introduction of a new IGRT application, which integrates quality management tools widely recognized for their role in risk mitigation: automation of the data transfer and workflow steps, and with the introduction of checklists and redundancy cross‐checks.