Agoforestry has been an importance alternative in land management system to improve rural livelihoods. Timber and Non-timber Forest Products (NTFPs) have been the most important components in agroforestry system, and to rural villagers’ household income portfolio, including in Java and Eastern Indonesia. However, the marketing strategy for these two components at the household level has been quite disintegrated and resulted in low benefit margins along the value chain continuum. Eventually, the low benefit margins are perceived by rural households as unattractive incentives to improve their integrated management practices at farming level, and households tend to cultivate more on products that are highly demanded by the market. This could lead to less diversified agroforestry system. Realising this critical problem, a value chain analysis of timber and NTFPs is needed to ensure integrated marketing of timber and NTFPs which in turn will improve the rural livelihoods. Through a better understanding of different products value chains, locally tailored interventions could be promoted to ensure more cost-effective and strategic value chains in improving households’ profit margins of various products under integrated agroforestry system. Preliminary analysis has indicated there is a limited involvement of local households in value-added activities of different products due to a lack of understanding of products demanded by the market. With regard to timber, lack of understanding on relevant policy and regulations has been the main constraint. Intervention should be directed to improve local villagers’ knowledge and capacity to understand the market characteristics of both timber and NTFPs and on how to optimize the seasonal calendar of the different products with a fluctuated market demand for sustainable income along the year.