The GEDI LiDAR system was specifically designed to detect vegetation structure and has proven to be a suitable tool for estimating forest biophysical parameters, especially canopy height, at a global scale. This study compares the GEDI relative height metric (RH100) over different forest types, especially deciduous broadleaf and evergreen coniferous located in Thuringia, Germany, to understand how the forest structural differences affect the GEDI height estimation. A canopy height model that was produced using digital terrain and surface models (DTM and DSM) derived from airborne laser scanning data is used as the reference data. Based on the result, GEDI canopy height over needleleaf forest is slightly more accurate (RMSE = 6.61 m) than that over broadleaf (RMSE = 8.30 m) and mixed (RMSE = 7.94 m) forest. Evaluation of the GEDI acquisition parameters shows that differences in beam type, sensitivity, and acquisition time do not significantly affect the accuracy of canopy heights, especially over needleleaf forests. Considering foliage condition impacts on canopy height estimation, the contrasting result is observed in the broadleaf and needleleaf forests. The GEDI dataset acquired during the winter when deciduous species shed their leaves (the so-called leaf-off dataset), outperforms the leaf-on dataset in the broadleaf forest but shows less accurate results for the needleleaf forest. Considering the effect of the plant area index (PAI) on the accuracy of the GEDI canopy height, the GEDI dataset is divided into two sets with low and high PAI values with a threshold of median PAI = 2. The results show that the low PAI dataset (median PAI < 2) corresponds to the non-growing season (autumn and winter) in the broadleaf forest. The slightly better performance of GEDI using the non-growing dataset (RMSE = 7.40 m) compared to the growing dataset (RMSE = 8.44 m) in the deciduous broadleaf forest and vice versa, the slightly better result using the growing dataset (RMSE = 6.38 m) compared to the non-growing dataset (RMSE = 7.24 m) in the evergreen needleleaf forest is in line with the results using the leaf-off/leaf-on season dataset. Although a slight improvement in canopy height estimation was observed using either the leaf-off or non-growing season dataset for broadleaf forest, and either the leaf-on or growing season dataset for needleleaf forest, the approach of filtering GEDI data based on such seasonal acquisition time is recommended when retrieving canopy height over pure stands of broadleaf or needleleaf species, and the sufficient dataset is available.