Agroforestry (AF)-based adaptation to global climate change can consist of (1) reversal of negative trends in diverse tree cover as generic portfolio risk management strategy; (2) targeted, strategic, shift in resource capture (e.g. light, water) to adjust to changing conditions (e.g. lower or more variable rainfall, higher temperatures); (3) vegetation-based influences on rainfall patterns; or (4) adaptive, tactical, management of tree-crop interactions based on weather forecasts for the (next) growing season. Forty years ago, a tree physiological research tradition in aboveground and belowground resource capture was established with questions and methods on climate-tree-soil-crop interactions in space and time that are still relevant for today’s challenges. After summarising early research contributions, we review recent literature to assess current levels of uncertainty in climate adaptation assessments in and through AF. Quantification of microclimate within and around tree canopies showed a gap between standard climate station data (designed to avoid tree influences) and the actual climate in which crop and tree meristems or livestock operates in real-world AF. Where global scenario modelling of ‘macroclimate’ change in mean annual rainfall and temperature extrapolates from climate station conditions in past decades, it ignores microclimate effects of trees. There still is a shortage of long-term phenology records to analyse tree biological responses across a wide range of species to climate variability, especially where flowering and pollination matter. Physiological understanding can complement farmer knowledge and help guide policy decisions that allow AF solutions to emerge and tree germplasm to be adjusted for the growing conditions expected over the lifetime of a tree.