Tropical agroforestry systems support the wellbeing of many smallholder farmers. These systems provide smallholders with crops for consumption and income through their ecological interactions between their tree, soil, and crop components. These interactions, however, could be vulnerable to changes in climate conditions; yet a reliable understanding of how this could happen is not well documented. The aim of this study is to understand how tree-soil-crop interactions and crop yield are affected by changes in climate conditions, which has implications for recognising how these systems could be affected by climate change. We used a space-for-time climate analogue approach, in conjunction with structural equation modelling, to empirically examine how warmer and drier climate conditions affects tree-soil-crop interactions and banana yield in Mt. Kilimanjaro's homegarden agroforest. Overall, the change in climate conditions negatively affected ecological interactions in the homegardens by destabilizing soil nutrient cycles. Banana yield, however, was mainly directly influenced by the climate. Banana yields could initially benefit from the warmer climate before later declining under water stress. Our findings imply that under increasingly warmer and drier climate conditions, homegarden agroforestry may not be a robust long-term farming practice which can protect smallholder's wellbeing unless effective irrigation measures are implemented.