Habitat Directive is the core strategy of nature conservation in Europe aiming at halting biodiversity loss. In this study the results of the third Italian assessment regarding the conservation status (CS) of plants listed in the Habitat Directive (Flora of community interest—FCI) was presented. Data was collected from several sources related to plant distribution, population data, habitats and pressures. Following the official European procedure, all parameters were evaluated and combined to give the CS of each taxon in each biogeographical region of presence. A comparison between the recent Italian IUCN and Reporting assessments was performed in order to evaluate the consistency between these two assessments. The official EU checklist comprises 113 Italian plant taxa, 107 of which were examined in this study. Our results showed a critical situation with only 34% of favourable CS, while 50% were unfavourable (40% inadequate plus 10% bad) and 16% unknown, in particular in the Mediterranean bioregion, where the unfavourable assessments reach the 65%. The results of the Report were consistent with those of the IUCN assessment, in which 41.9% of plants were threatened with extinction. This report highlighted some benefits and criticisms at national level, but it may have a wider significance. Although a general advance of knowledge, a great effort is needed to reach the Habitats Directive goals. Despite the limited resources, monitoring activities needs to be improved in order to close information gaps for several plants. A positive outcome was the development of a specific national project funded by the Italian Ministry of Environment, with the ambitious target to set future monitoring activities for FCI and optimize monitoring efforts.