Historical land-use changes shape present-day biodiversity through legacy effects, but the duration and mechanisms of these legacies are poorly understood. We used historical land-use maps in two Swedish landscapes across three centuries to examine the persistent influence of historical land use on plant and soil microbial communities. Overall, bacteria showed stronger legacy effects than fungi, but effects varied across functional groups of plant-associated and free-living taxa. However, soil-borne plant pathogenic fungi showed a persisting influence of arable land use which gradually disappeared after ~150 years, suggesting that land-use legacies decay over time. This dilution could relate to changing plant communities but also to changes in microbial associations, as suggested by species co-occurrence patterns over time. Our findings provide novel and crucial information on the duration of land-use legacies and single out soil-borne plant pathogens as key indicator groups of historical land use in present-day ecosystems.