The Churches and Monasteries are the main sites for biodiversity and forests conservation in Ethiopia. However, the loss of biodiversity and forest degradation is the most burning issue in Ethiopia as well as in Gonje Thewodros Monastery Forest (GTMF), because of anthropogenic and naturally induced disturbances. Thus, this study was aimed at evaluating the woody species composition, vegetation structure and regeneration status of GTMF in Gonje Kolela district. A Systematic random sampling designs were employed to set sampling plots for vegetation data collection. I have used Shannon-Weiner diversity index and Sorensen similarity coefficient for analysis of data. Five sampling transect lines and the total of (14,000 m2) 35 main sampling plots and (4375m2 and 175m2) 175 sub-plots were used to collect matured, saplings and seedlings woody plant species, respectively. The GTMF had three different types of communities were classified based on the dominant woody plant species. A total of 62 woody plant species belonging to 52 genera and 34 families were recorded and identified. The majority of the woody plant species were shrubs (50%) and the remaining were trees and climbers contributed 37% and 13%, respectively. GTMF had 3.5 and 0.85 the Shannon-Weiner diversity index and evenness value, respectively. The percentage of Sorensen similarity coefficient among communities ranges from 43.3% - 66.7%. Out of 62 woody plant species, 6.5% and 71% were endemic and had fair regeneration status, respectively. In this study, the degree of dominance and abundance of woody plant species was not equal in their IVI. Therefore, GTMF had great role in conservation of biodiversity. However, currently, the GTMF is under anthropogenic and naturally induced disturbances. The majority anthropogenic induced disturbance were grazing, farm land expansion to the monastery as well as residents and selective cuttings of trees and shrubs. Generally, the Monastery forest is under severe threat due to diversity of factors. Therefore, protection of plant diversity through different and feasible conservation strategies Such as finding alternative for grazing and farmlands and avoiding selective cutting of trees is recommended.