Deployment of an on-site laboratory to contain an expanding outbreak and protect public health through rapid diagnosis of infected patients and identification of their contacts is a challenging and complex response, further complicated by time limitation and dramatic consequences of failure. Effective operations management and decision-making are critical for a successful Fieldable Laboratory (FL) mission at each phase of the mission. To analyze the principles and challenges of the operations management and associated decision-making process, the FL mission has been broken down into five successive interlinked phases defined as the "FL mission cycle" (FL-MC). Each phase comprises a set of operational functions (OFs) corresponding to the mission activities. Some decisions are associated with a single OF, whereas others are taken across different OFs and FL-MC phases. All decisions are treated as logical entities inherently linked to each other and to the whole situational context within the FL operational domain. Being part of the laboratory information management system (LIMS), the FL domain ontology is developed as the main knowledge management tool supporting the decision-making process. This is an essential way to promote interoperability and scalability between different FL modules and health care capacities during cross-border biological crises.