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The biodiverse montane forests of the tropical Andes are today frequently disturbed by rainfall-driven mass movements which occur mostly during extreme El Ni~no events. Over the coming decades these events are projected to double under the 1.5  C global warming scenario. The consequent increased rainfall and mass movement events likely present an elevated risk to millions of people living in the Andes. However, the impact of more frequent rainfall extremes remains unclear due to a lack of studies that directly link past changes in El Ni~no-Southern Oscillation (ENSO) frequency to forest and landscape disturbance patterns. Here, we present the first Holocene palaeoecological record from Laguna Pallcacocha, southern Ecuador, a key site for El Ni~no reconstructions. We demonstrate that for the past 10,000 years plant taxa indicative of recolonization e such as Alnus acuminata e covary with El Ni~no-induced flood layers in the lake. An amplified forest disturbance pattern is observed in the late Holocene, suggesting enhanced slope instability following deforestation. The temporal pattern is not explained by tree line fluctuations or human impact, while the latter does amplify the impact of ENSO on landscape disturbance. Spatial correlations between modern ENSO and precipitation are consistent with a regional comparison of Holocene records of landscape disturbance. Our results indicate that climate extremes, such as those associated with future intensification of El Ni~no, combined with ongoing land use change will increase the frequency of mass movements elevating risks for millions of people in the Andes.