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Ecosystem services have been steadily incorporated into policy and planning, particularly for conservation. While biophysical and economic values are often part of ecosystems assessments, integrating participatory approaches with these valuation tools into planning is essential. This study demonstrates the importance of undertaking case studies with an integrated approach from valuation to practice. We focus on the evaluation of ecosystem services based on user priorities in three different countries that comprise the northwestern part of the Amazon basin: Colombia, Ecuador, and Peru. A total of 473 community and government representatives were interviewed and their priorities for ecosystem services were elicited. We used three approaches to value the prioritized services, market prices, cost avoided, and the value transfer method. We linked the economic valuation results with policy and development alternatives that focus on ES management and we utilized an adaptive policy framework as a crucial step to assess the “trade off” in relation to any given economic, social, and environmental goal. Seven ecosystem services were identified as priorities: fish, timber, and non-timber forest products as provisioning services; disease regulation, water purification, and carbon sequestration as regulating services; and scenic beauty as the only cultural service. The ecosystem services contributing to the highest proportion of local GDP were regulation of malaria (3.9%) in Colombia, followed by ecotourism (1.75%) in Ecuador and fish (1.7%) in Peru. The instruments developed to help integrate this information into policy actions are mostly related to improving the property right systems currently implemented in each country. The results of this study will enable the management of ecosystem service values to be targeted in planning development at the subnational level in each country.