The long-term resilience of Pyrenean forests in the face of historical anthropogenic clearing remains largely unknown. The palynological study of the varved sediments from a mid-elevation (1027 m) karstic lake provides a high-resolution record of three major century-scale deforestation/recovery (DR) cycles that occurred in the last two millennia, during Roman, Medieval and Modern times. Each DR cycle is characterized considering three different levels: overall forest trends, by forest type and by individual taxa. Overall, the studied forests exhibited high resilience, as they recovered almost completely after each deforestation event (bulk resilience). The critical point of no return (tipping point) beyond which forests would have irreversibly disappeared from the region was never reached, even after deforestation magnitudes above 60%. The different forest types identified (conifer, sclerophyll and deciduous) persisted over time, showing similar heterogeneous patterns with minor spatial reorganizations (mosaic resilience). Individually, the main forest taxa underwent minor variations in their relative abundances, always within the same attraction domains (community resilience). The high levels of resilience documented in these Pyrenean forests are attributed to the action of metapopulation and metacommunity processes and mechanisms in a highly dynamic patchy environment. Conservation actions should be focused on the maintenance of these spatial patterns and the associated ecological dynamics.