The process of secondary succession is one of the most significant threats to non-forest (natural and semi-natural open) Natura 2000 habitats in Poland; shrub and tree encroachment taking place on abandoned, low productive agricultural areas, historically used as pastures or meadows, leads to changes to the composition of species and biodiversity loss, and results in landscape transformations. There is a perceived need to create a methodology for the monitoring of vegetation succession by airborne remote sensing, both from quantitative (area, volume) and qualitative (plant species) perspectives. This is likely to become a very important issue for the effective protection of natural and semi-natural habitats and to advance conservation planning. A key variable to be established when implementing a qualitative approach is the remote sensing data acquisition date, which determines the developmental stage of trees and shrubs forming the succession process. It is essential to choose the optimal date on which the spectral and geometrical characteristics of the species are as different from each other as possible. As part of the research presented here, we compare classifications based on remote sensing data acquired during three different parts of the growing season (spring, summer and autumn) for five study areas. The remote sensing data used include high-resolution hyperspectral imagery and LiDAR (Light Detection and Ranging) data acquired simultaneously from a common aerial platform. Classifications are done using the random forest algorithm, and the set of features to be classified is determined by a recursive feature elimination procedure. The results show that the time of remote sensing data acquisition influences the possibility of differentiating succession species. This was demonstrated by significant differences in the spatial extent of species, which ranged from 33.2% to 56.2% when comparing pairs of maps, and differences in classification accuracies, which when expressed in values of Cohen’s Kappa reached ~0.2. For most of the analysed species, the spring and autumn dates turned out to be slightly more favourable than the summer one. However, the final recommendation for the data acquisition time should take into consideration the phenological cycle of deciduous species present within the research area and the abiotic conditions.