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Montados are silvo-pastoral systems, typical of the western Mediterranean Basin. When well managed, these ecosystems provide relevant ecosystem services and biodiversity conservation. In the northern part of the Mediterranean Basin, cork oak areas are mainly privately owned and a source of income to landowners, chiefly through cork and livestock production. Sustainable use is essential to maintain the ecological sustainability and socio-economic viability of these ecosystems. Biodiversity conservation and non-provisioning ecosystem services may generate additional incentives promoting sustainable use and conservation of montados, but require adequate mapping and identification. The high conservation value forest (HCVF) framework allows systematic inventory of biodiversity and non-provisioning ecosystem services and is widely applied in forest ecosystems. Here we exemplify the application of HCVF to the cork oak landscape of southern Portugal using a WebGIS tool that integrates the HCVF framework, in conjunction with Pareto optimization, to identify areas important for the conservation of biodiversity and ecosystem services. We present a case study using threatened bird and reptile species, as examples of biodiversity attributes, and carbon storage and water recharge rate of aquifers, as examples of ecosystem services attributes. We identify those areas in a cork oak landscape of southern Portugal where biodiversity and ecosystem services attributes are optimized. These areas can be prioritized for implementing conservation mechanisms, such as payment for ecosystem services, to promote sustainable forest management.