Among the main objectives of Natura 2000 Network sites management plans is monitoring their conservation status under a reasonable cost and with high temporal frequency. The aim of this study is to assess the ability of single-photon light detection and ranging (LiDAR) technology (14 points per m2) and Sentinel-2 data to classify the conservation status of oak forests in four special areas of conservation in Navarra Province (Spain) that comprise three habitats. To capture the variability of conservation status within the three habitats, we first performed a random stratified sampling based on conservation status measured in the field, canopy cover, and terrain slope and height. Thereafter, we compared two metric selection approaches, namely Kruskal–Wallis and Dunn tests, and two machine learning classification methods, random forest (RF) and support vector machine (SVM), to classify the conservation statuses using LiDAR and Sentinel-2 data. The best-fit classification model, which included only LiDAR metrics, was obtained using the random forest method, with an overall classification accuracy after validation of 83.01%, 75.51%, and 88.25% for Quercus robur (9160), Quercus pyrenaica (9230), and Quercus faginea (9240) habitats, respectively. The models include three to six LiDAR metrics, with the structural diversity indices (LiDAR height evenness index, LHEI, and LiDAR height diversity index, LHDI) and canopy cover (FCC) being the most relevant ones. The inclusion of the NDVI index from the Sentinel-2 image did not improve the classification accuracy significantly. This approach demonstrates its value for classifying and subsequently mapping conservation statuses in oak groves and other Natura 2000 Network habitat sites at a regional scale, which could serve for more effective monitoring and management of high biodiversity habitats.