Recent research on deforestation in the Brazilian Amazon has rarely included empirical observation of how land managers perceive and respond to forest governance rules. In this case study, we consider how two decades of pilot projects for integrated conservation and sustainable development (ICDPs) variously influenced forest governance across three agrarian reform settlements in northwestern Mato Grosso state. The analysis combines: i) remote sensing of deforestation from 1997–2015; ii) land use and economic data for individual settler farms and cooperatives; iii) settlers' perceptions regarding legitimacy and relevance of state policies, including land use regulations under the Brazilian Forest Code. Deforestation across settlements varied in association with synergies – or lack thereof – between policy instruments and socially embedded rules organizing economic alternatives to the dominant regional pattern of cattle ranching. In two of the settlements deforestation surpassed or was approaching 80% of their total area. In the third settlement deforestation stabilized at 45%, corresponding with the initiation of ICDP support for a pilot project focused on Brazil nut extractivism to consolidate community management of the settlement's collective forest reserve. The latter process involved a ‘policy mix’ or sequence of overlapping components: technical assistance, cooperative organization, environmental licensing, infrastructure, equitable contracts with surrounding indigenous communities and market development. Comparing with the two counterfactual cases, we suggest a framework for analysis of systemic socio‐ecological change in settlements in the Brazilian Amazon, and reconsider the role of ICDPs in landscape approaches to environmental governance in tropical forests. Copyright © 2017 John Wiley & Sons, Ltd and ERP Environment