The management of people’s health and safety in cultural buildings has been drastically changed in view of the COVID-19 pandemic. The combined effects of crowding levels and people’s flows are now associated not only with emergency conditions (i.e., evacuation) but also with ordinary fruition issues, given the possible spreading of the virus. Cultural buildings, particularly cultural heritage, are critical scenarios for emergency and fruition issues because of their specific geometric and technical features. They suffered from COVID-19 restrictions mainly due to physical distancing measures. Protocols have been developed during the last two years to manage pandemics in such contexts, and the increasing number of vaccinated people is also pushing toward a full return to pre-pandemic rules. However, they should be carefully evaluated and tailored depending on cultural heritage conditions. This work identifies and evaluates combined measures to manage people’s flows (access, movement, queue) depending on boundary conditions at the overall (building capacity) and individual levels (face mask; vaccinated/recovered; “green pass”). The effectiveness evaluation is performed by using a simulation model that jointly represents the virus spreading and the people’s flow. An Italian historical arena is selected as a significant case study. Results show that a higher occupants’ number can multiply the contagion spreading. Still, a more significant impact on its limitation can be achieved by controlling infectors’ access (supporting body temperature control with rapid tests) and occupants’ movement during queues and pauses. The methodology can help decision-makers to balance a proper combined application of management measures.