Ecosystem-based Adaptation (EbA) is a strategy that relies on forest landscape’s biodiversity management and restoration to enhance the sustainable production and supply of ecosystem goods and services as alternative livelihoods to cushion the society against the negative impacts of climate change. As climate change becomes a reality, adaptation measures which are cost effective and economically beneficial are urgently required. Mount Elgon ecosystem in the western region of Kenya has EbA characteristics which could offer longer term solutions to adaptation to climate change impacts while providing a range of other benefits in terms of ecosystem goods and services. This paper established the existing capacities for Ecosystem based adaptation inclusion in the sub-national adaptation plans and policies in order to improve resilience to climate change impacts in the Mt. Elgon ecosystem. To achieve this, a descriptive survey was carried involving 405 household and 51 government and civil society respondent drawn from Saboti, Kiminini, Endebess and Kwanza sub-counties, Transnzoia County in Kenya. Results showed that there were good institutional representations in Mt. Elgon ecosystem with line ministries largely being responsible (63.4%) for the management of the individual natural resources that occur in the Mt. Elgon ecosystem while a few others were either co-managed (9.7%) or managed by the County Government of Transnzoia (9.7%). Majority (77%) of household respondents observed uncoordinated approach in ecosystem management. This should be addressed in order to increase ecosystem health which eventually leads to enhanced EbA services. Majority (73.2%) of government and civil society respondents cite inter-sectoral policy inconsistencies and conflicts as contributors to degradation of ecosystem health in the study area. This too has impacted negatively on EbA. A major conclusion in the study was that consolidation and harmonization of ecosystem policies in the Mt. Elgon’s ecosystem will lead to a healthy landscape that provides sustainable EbA services.