He was then imprisoned for some time because his radical approach to archaeology and strong nationalist feelings landed him in trouble with the king of Naples, Ferdinand II.
With the unification of Italy in 1860, the legal status of Pompeii changed from being a royal possession from which monarchs could use the site to obtain antiquities for their private collections or to gift artifacts to illustrious foreign guests, to property of the state.
Fiorelli was named superintendent and he began to manage the excavations to transform Pompeii into a place to visit to gain a glimpse into the past of western civilization and begin to understand those who went before the modern world.
In this way the data collected during the excavations could be used to help with the restoration of the ancient buildings and of their interiors — although the most important wall paintings and mosaics still continued to be stripped and transported to Naples.
He founded a training school where foreigners as well as Italians could learn archaeological technique, and made a particular study of the materials and building methods used in Pompeii.
His work at Pompeii was continued by Michele Ruggiero, Giulio De Petra, Ettore Pais and Antonio Sogliano, who began to restore the roofs of the houses with wood and tiles in order to protect the remaining wall paintings and mosaics inside.