CubeSats provide opportunities for science and technology demonstration missions with low-cost solutions and short project timescales, in particular, for studying gamma-ray bursts (GRBs) in the multi-messenger era. A robust operations strategy for scientific CubeSat projects is key to optimizing the results obtained from the experimental instruments. The Educational Irish Research Satellite-1 (EIRSAT-1) is a 2U CubeSat with three payloads, including a bespoke gamma-ray detector, gamma-ray module (GMOD), developed in-house for the detection of GRBs. The detection and reporting of GRB triggers to the scientific community complicates and drives the mission operational strategy. The operational procedures developed for commissioning and operating GMOD are detailed. The successful operation of EIRSAT-1 will facilitate the detection of ∼15 GRBs∕year in low Earth orbit. To increase the likelihood of mission success, the project is following a prototype model philosophy, building, and testing, both an engineering qualification model (EQM) and flight model. The EIRSAT-1 operations manual is the document that will instruct operators in commanding the spacecraft correctly and efficiently throughout the mission lifetime. The operations manual must be refined in parallel to payload development. This two-model philosophy has provided time for the early development of the EIRSAT-1 operations manual with the EQM. The EIRSAT-1 operations manual has undergone incremental updates based on feedback from operational development tests (ODTs), and a version with 35 procedures was frozen prior to the month-long EQM mission test (MT). Specifically, the objective of our work is to validate and refine the operations manual using the EQM MT process. Although the ODTs were effective preparation, the MT process highlighted issues, such as procedures operators found convoluted, and scenarios not yet considered during the initial development stages. Two new procedures were identified, 8 procedures required major updates, 15 required minor updates, and the remaining 12 required no improvements after the MT. The validation process facilitated operator training in mission representative conditions, such as GRB triggering data downlink with GMOD, and the major lessons learned during the development and validation process are presented.