This study analysed the dynamics of natural habitat types in the last 30 years, in the three largest Natura 2000 sites in the Apuseni Mountains area in Romania. The Apuseni Mountains area records one of the highest percentages of protected areas among Romanian mountains, exceeding 50%, characterised by high biodiversity with faunal and floral endemics and rare species across distinctive karstic landscapes. Habitat type maps were derived from Landsat satellite images acquired in 1986, 1993, 2000, 2007 and 2015 using an object-based classification. Based on habitat type maps, 18 landscape metrics at the class level and 16 metrics at the landscape level have been derived to quantify the structure, composition and spatial pattern of the landscape, correlating them with habitat type area changes. Results indicate that in the last 30 years, the deciduous and coniferous forests continuously improved in the Apuseni-Vlădeasa Mountains, but surprisingly deteriorated after the site was declared a Special Protection Area (SPA) in 2007. The mixed forest habitat type has recorded a tendency of deterioration since 1986, however, this trend stopped in 2007, probably due to the decrease of human interventions. In this site, the pastures and meadows habitat type deteriorated until 2000 due to agriculture development (before 1993) and natural growth of vegetation, improving considerably after that with a surprising atenuation after 2007. The deciduous forests habitats within the Defileul Mureşului Inferior – Dealurile Lipovei site deteriorated until 2007, but it appears that human interventions have diminished after the site was declared a SPA, while within the Drocea-Zarand site the deciduous forests have not suffered deterioration. In these two sites, pastures recorded a constant deterioration in the last three decades, mainly due to land abandonment. Results are potentially useful for authorities to improve management and to develop appropriate strategies for habitat conservation. •Dynamics of natural habitat types of the Apuseni Mountains since 1986 were analyzed.•Habitat types condition in the largest site improved in the last 30 years.•The largest site landscape has been alarmingly deteriorated after the site was declared a Special Protection Area.•The other two sites recorded overall tendencies of habitat type deterioration.