The use of hyperspectral (HS) and LiDAR acquisitions has a great potential to enhance mapping and monitoring practices of endangered grasslands habitats, beyond conventional botanical field surveys. In this study we assess the potentiality of recursive feature elimination (RFE) in combination with random forest (RF) classification in extracting the main HS and LiDAR features needed to map selected Natura 2000 grasslands along Polish lowland river valleys, in particular alluvial meadows 6440, lowland hay meadows 6510, and xeric and calcareous grasslands 6120. We developed an automated RFE-RF system capable to combine the potentials of both techniques and applied it to multiple acquisitions. Several LiDAR-based products and different spectral indices (SI) were computed and used as input in the system, with the aim of shedding light on the best-to-use features. Results showed a remarkable increase in classification accuracy when LiDAR and SI products are added to the HS dataset, strengthening in particular the importance of employing LiDAR in combination with HS. Using only the 24 optimal features selection generalized over the three study areas, strongly linked to the highly heterogeneous characteristics of the habitats and landscapes investigated, it was possible to achieve rather high classification results (K around 0.7–0.77 and habitats F1 accuracy around 0.8–0.85), indicating that the selected Natura 2000 meadows and dry grasslands habitats can be automatically mapped by airborne HS and LiDAR data. Similar approaches might be considered for future monitoring activities in the context of habitats protection and conservation.