The prehistoric architecture of Sardinia (Italy) is characterized by the outstanding phenomena of hypogeism and megalithism. Hypogeism finds its maximum expression in the domus de janas (houses of the fairies), collective tombs carved into the rock with stone tools. The domus de janas mainly date back to the recent Neolithic, but their excavation continued up to the Copper Age, and sometimes their reuse reached up to the Middle Ages. There are about 3500 domus de janas, spread almost throughout Sardinian territory. The promotion of the domus de janas as UNESCO World Heritage is currently underway and requires information relating to the current state of conservation of the monuments to define the interventions necessary to make the monuments enjoyable in a sustainable way protecting them from natural and anthropic hazards, allowing cultural fruition, and preserving at the same time the values of authenticity and identity of sites. In this framework, a methodology for the restoration and structural safety of the domus de janas object of the UNESCO candidacy has been implemented, articulated in three main points: (I) the analytical study of the monuments, including survey activities, mapping, diagnostics, and critical analysis aimed at assessing their state of conservation; (II) the proposal of guidelines for conservation and material and structural restoration through the definition of key indicators for the measurement and evaluation of the state of conservation of the monuments and the factors that influence it; and (III) the identification of the measures for the conservation and the mitigation of environmental risks relevant to the archaeological monuments, along with the periodicity of the monitoring. This article illustrates and discusses the proposed methodology also with reference to a case study.