Multiscale Boiling is a European Space Agency funded experiment performed on-board the International Space Station between 2019 and 2021 that aimed at studying the basic physics of the boiling process. This paper focuses on the operational aspects of the Multiscale Boiling experiment, from its preparation to the execution on-board of the ISS and the lessons learnt. Studying boiling in a microgravity environment allows studying the basic physical aspects of the boiling process and allows the observation of effects that are too fast and too faint to be measured under normal gravity conditions. The experiment addresses fundamental questions about two-phase heat transfer during boiling processes. For this purpose, single or few subsequential bubbles are selectively ignited in a nucleation point on a heated substrate using a short laser pulse. A multi-scale experimental approach is adopted, including the application of two external forces (electrical field and shear flow). The diagnostics tools include a multi-thermocouple rack, high-speed black and white and infrared cameras. More than 3000 data sets have been generated over a 9-month measurement period spread over two measurement campaigns. The experiment was monitored and controlled from ground by the Belgian User Support Operations Centre (B.USOC) and the raw scientific data was further distributed to the Science Teams. The process of boiling heat transfer depends on the environmental conditions, determined by the liquid temperature, the liquid pressure, the heat flux at the substrate heater, the preheating time, the liquid flow rate, and the strength of the electric field. This large number of experiment parameters results in a complex setup which requires careful monitoring and continuous real-time control by the ground operator, preventing a fully automated approach for the science runs. The Multiscale Boiling experiment was operationally challenging, as the conduct and result of the experiment was mainly relying on the expertise of the ground operator. An assessment was made of the operational issues that had to be dealt with during both the operations preparation and execution phases with recommendations to the processes applied over the lifetime of such a project. In addition, during the operations execution, several hardware anomalies occurred, preventing the complete achievement of all mission objectives while additional objectives were added to compensate for it. Nevertheless, the Science Teams are very satisfied with the data, which are of an unprecedented quality. The data will be used to achieve a much better knowledge about the boiling process and to validate theoretical models and numerical codes. The success of the mission was made possible thanks to the intense and productive close collaboration between the different instances involved, being the international and multidisciplinary Science Teams, the European Space Agency (ESA), Airbus and the B.USOC.