Recent land-use and climatic shifts are expected to alter species distributions, the provisioning of ecosystem services, and livelihoods of biodiversity-dependent societies living in multifunctional landscapes. However, to date, few studies have integrated social and ecological evidence to understand how humans perceive change, and adapt agro-ecological practices at the landscape scale. Mixed method fieldwork compared observed changes in plant species distribution across a climatic gradient to farmers’ perceptions in biodiversity and climate change in rice-cultivated farms. In contrast to the global context, farmers in the Terai Plains of Nepal are acutely aware of high levels of change observed in the last 10 years, and incrementally adapt as new invasive species emerge (93%), the incidence and severity of pest/diseases increase (66%), genetic diversity of indigenous varieties erodes (65%), forest habitats diminish (98%), irrigation water declines (60%), and wildlife ranges shift. Twenty-five changes in climate were reported by 97.5% of farmers to reduce provisioning services and food self-sufficiency, and increase exposure to waterborne pathogens, heat stress, and human or livestock mortality. The study illustrates the need for financial and institutional supports at all levels to strengthen agro-ecological practices, upscale Information Communication Technology for extension services, clarify tenure agreements, and safeguard natural ecosystems to slow biodiversity loss. Existing incentives to conserve, restore, or sustainably manage ecosystems offer lessons for other societies undergoing rapid change.Electronic supplementary materialThe online version of this article (10.1007/s13280-019-01202-0) contains supplementary material, which is available to authorized users.