Coffee agroforestry systems are intermediate between forest and monoculture coffee in many aspects of above and belowground biodiversity and related functions. For the farmer, however, the balance of positive and negative aspects of diversity needs to be understood in relation to key processes such as nutrient and water uptake, slope and topsoil integrity and harvestable yield. Climate variability affects water availability, modulated by the pattern of infiltration and water holding capacity of the soil, but also through pest and disease relationships that influence root functions in water uptake. In the Way Besai catchment (Sumberjaya, Lampung, Indonesia) that has seen a rapid transformation towards coffee in the past 3 decades, we surveyed earthworm, nematode and termite diversity profiles of forest, coffee agroforestry, simple shade-tree + coffee mixtures and coffee monocultures were combined with measurement of soil macroporosity, surface runoff and coffee yields. Four relatively large-bodied native earthworms were lost upon forest conversion, with six exotic and smaller-bodied worms replacing them. The nematode fauna shifted towards plant-parasitic genera, especially where a grass/weed understory was present. Shade trees depress ground vegetation through litter, reducing plant parasitic nematodes, but enhancing earthworms. Gliricidia sepium, a favourite  N₂ fixing companion tree of coffee is toxic for earthworms as well as plant parasitic nematodes, while banana stimulates the nematodes but provides direct yield to the farmer. Termites can shift from beneficial to pest status depending on the availability of woody debris in the system. Overall, the multispecies coffee agroforestry systems are more robust to climate variability, partially through these biotic interactions with soil fauna. Farmer knowledge tends to focus on what is visible aboveground and rationalizes the benefits and negative impacts of various companion trees in terms of ‘hot’ or ‘cold’ soil properties. Although these terms do not directly relate to temperature, management towards ‘cold’ components can in fact buffer them from effects of global warming.