The FragmentatiOn mymargin Of Target (FOOT) experiment aims to provide precise nuclear cross section measurements for two different fields: hadrontherapy and radio-protection in space. The main reason is the important role the nuclear fragmentation process plays in both fields, where the health risks caused by radiation are very similar and mainly attributable to the fragmentation process. The FOOT experiment has been developed in such a way that the experimental setup is easily movable and fits the space limitations of the experimental and treatment rooms available in hadrontherapy treatment centers, where most of the data takings are carried out. The trigger and data acquisition system needs to follow the same criteria and it should work in different laboratories and different conditions. It has been designed to acquire high statistics samples to fulfill the accuracy requirements of the physics analysis. Data-taking is being monitored online to allow the shift crew to verify the correct functioning of the system.