The forests of the Zegie Peninsula and the nearby monastic islands of Lake Tana constitute a bioculturally, economically, and environmentally important remnant of Afromontane Forest in northwestern Ethiopia. These forests harbor high woody species diversity, store substantial amounts of carbon, and sustain long-established indigenous knowledge systems related to medicinal plant use and coffee-based agroforestry. Despite their ecological and cultural importance, the forests are increasingly threatened by anthropogenic pressures, necessitating an integrated ecological and ethnobotanical assessment. This monograph synthesizes findings from four interrelated objectives: assessment of woody species diversity, vegetation structure and regeneration; estimation of aboveground and belowground biomass and carbon sequestration potential; documentation of medicinal plant diversity and use patterns as well as threats to medicinal plants; and evaluation of indigenous shade tree species selection and management practices in coffee agroforestry systems.Vegetation and carbon stock data were collected from 165 systematically established plots across the Zegie Peninsula and three monastic islands (Kebran Gebriel, Entons Eyesus, Daga Estifanos). Ethnobotanical information was gathered through semi-structured interviews, focus group discussions, key informant interviews, and guided field walks. A total of 162 woody species, 81 medicinal plant species, and 20 shade tree species were recorded, confirming the exceptional biological and cultural richness of the study area. The forests exhibited high species diversity, relatively balanced population structures, and generally healthy regeneration patterns, although several ecologically and economically important species showed poor regeneration. Mean total carbon stock was estimated to be 196.4 tons C ha⁻¹, highlighting the strong climate change mitigation potential of these forests. Carbon storage varied significantly among sites and was more strongly influenced by topographic factors than by classical biodiversity metrics. The low contribution of soil physicochemical characteristics (31.3%) to species spatial variation indicates that anthropogenic pressures and natural disturbances play a major role in shaping the plant communities of the Zegie Peninsula and nearby monastic island forests. Generalized Linear Mixed Model (GLMM) analysis showed that selective cutting had a significant negative effect on species richness and seedling density, indicating that anthropogenic disturbance reduces biodiversity and limits natural regeneration, while stand density of mature trees remained relatively stable, suggesting a late response of forest structure to disturbance. Medicinal plant use was characterized by high informant consensus for common ailments, XIX reflecting deep-rooted traditional healthcare practices. However, ethnobotanical knowledge was unevenly distributed among social groups and showed signs of erosion, particularly among younger generations. Indigenous knowledge also played a central role in sustaining coffee-based agroforestry systems. Farmers applied complex ecological, functional, and cultural criteria in shade tree selection, favoring species that enhance coffee yield and soil fertility, minimal root competition, and microclimatic regulation. Monastic institutions was found as key custodians of indigenous tree species through long-standing religious norms and management practices. In general, the forests of the Zegie Peninsula and neighboring islands function as important biodiversity refugia, significant carbon sinks, and living repositories of indigenous knowledge on medicinal plants use and management as well as selection and management of shade tree species in coffee-based agroforestry system. Strengthening community-based conservation, promoting intergenerational knowledge transmission, and integrating carbon-focused incentive mechanisms with indigenous management practices are essential to ensure the long-term sustainability of these unique forest landscapes.