Climate change and a long legacy of fire suppression are leading to an increased prevalence of ‘mega‐disturbances’ such as drought and wildfire in terrestrial ecosystems. Evidence for the immediate effects of these novel disturbances on wildlife is accumulating, but little information exists on longer term impacts to species and ecosystems. We studied the occurrence dynamics of an iconic old‐forest species, the spotted owl (Strix occidentalis), on a long‐term study area in the Sierra Nevada, CA, USA from 1989 to 2020 to evaluate their multi‐scale population response following a 2014 megafire (the ‘King’ Fire) that affected a portion of our study area. We found that extensive severe fire within spotted owl sites resulted in both immediate site abandonment and prolonged lack of re‐colonization by owls six years post‐fire. Sites that experienced high pyrodiversity – a mosaic of burn severities – were more likely to persist after the fire, but this effect was only apparent at finer spatial scales. A potentially confounding factor, post‐fire salvage logging, did not explain variability in the probability of either owls persisting at sites or sites becoming re‐colonized; effects could be attributed only to severe fire extent and pyrodiversity. Our study demonstrates the prolonged effects of severe fire on the occupancy of this forest‐dependent species, suggesting that forest restoration that reduces megafires could benefit spotted owls. Our work emphasizes that long‐term monitoring can offer surprising learning opportunities and provide unparalleled value for understanding and addressing emerging environmental concerns.