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Land use change is a key driver of biodiversity change and plays out over extended spatiotemporal scales. Historical land-use changes may shape present-day microbial communities through legacy effects, but the duration and mechanisms underpinning these legacies are poorly understood. We used historical land use maps detailing land use changes between low-intensive arable land and grassland, and grassland and forest, respectively, in two Swedish landscapes across three centuries to examine legacy responses among soil microbial communities, especially on plant pathogenic taxa. Compared to fungi, the community structure of bacteria showed stronger legacy effects, which, however, largely disappeared within a century. Yet, the diversity and composition of soil-borne plant pathogenic taxa, especially among fungi, showed a persisting influence of arable land use that did not disappear until 150 years after land-use change, suggesting that a dilution occurs over time. This may be related to changes in microbial interactions driven by responses to disturbances, as suggested by species co-occurrence patterns over time. Our findings provide crucial information on the duration of microbial legacy effects in connection with land use and single out soil-borne plant pathogens as a key group to study to understand site history effects on long-term microbial community dynamics.