Agroforestry as active area of multi-, inter-, and transdisciplinary research aims to bridge several artificial divides that have respectable historical roots but hinder progress toward sustainable development goals. These include: (1) The segregation of “forestry trees” and “agricultural crops”, ignoring the continuity in functional properties and functions; the farm-scale “Agroforestry-1” concept seeks to reconnect perennial and annual, woody and nonwoody plants across the forest–agriculture divide to markets for inputs and outputs. (2) The identification of agriculture with provisioning services and the assumed monopoly of forests on other ecosystem services (including hydrology, carbon storage, biodiversity conservation) in the landscape, challenged by the opportunity of “integrated” solutions at landscape scale as the “Agroforestry-2” concept explores. (3) The gaps among local knowledge of farmers/agroforesters as landscape managers, the contributions of social and ecological sciences, the path-dependency of forestry, environmental or agricultural institutions, and emerging policy responses to “issue attention cycles” in the public debate, as is the focus of the “Agroforestry-3” concept. Progress in understanding social–ecological–economic systems at the practitioners–science–policy interface requires that both instrumental and relational values of nature are appreciated, as they complement critical steps in progressing issue cycles at the three scales. A set of hypotheses can guide further research.