The Grotta degli Animali in the garden of the Villa Medicea di Castello in Firenze is considered the first example of a rustic Mannerist artificial grotto. Its structure consists of a single vaulted chamber lined with spongy stones and decorated with pebbles, shells and animal sculptures made of various stone materials. The recent restoration project began with the results of an extensive diagnostic campaign. These results were used in the design of the restoration and further targeted investigations were carried out during the restoration. The knowledge base was completed with the installation of sensors to monitor environmental parameters (temperature, relative humidity, surface temperature of the sculptural elements and solar radiation) to study the impact of the micro-environmental changes on the conservation of the surfaces. Based on the case study, this paper describes the key aspects and the strategy that should be used to develop a plan for the risk assessment of the state of conservation of semi-confined environmental heritage assets. By the comparing of the monitoring data with the results of spot analysis carried out by portable and non-destructive instruments, and micro-sampling to characterize the constituent materials and alteration/decay products and archiving them in a digital twin, it is possible to define the guidelines and protocols for the management and preservation of heritage assets in a semi-confined environment.