After the initial infection, bacterial plant pathogens often localize to specific tissues or within certain parts of their hosts. In such cases, it may be possible to clear the infection by removing the infected portion and retraining the plant from the base of the trunk. We tested the efficacy of severe pruning at clearing grapevine infections by Xylella fastidiosa, the causal agent of Pierce’s disease. We surveyed vines in six Northern California vineyards and rated them on a scale of disease severity from 0 to 3. Next, we aggressively pruned vines by removing the trunk 10 cm above the graft union and we monitored their retrained canopies over time. Although 82% (284/346) of severely pruned vines appeared disease free the following season, the prevalence of symptoms in conventionally pruned control vines suggests that more than one-third (112/324) of vines would have recovered without severe pruning—at least those with less advanced symptoms. Moreover, for five of the six vineyards, the majority of severely pruned vines showed symptoms of Pierce’s disease by the time vines were retrained, two seasons after pruning (as high as 81%, 86/106; 71% overall, 245/346). These results suggest that severe pruning does not clear X. fastidiosa infection from grapevines to an extent that would justify its adoption for disease management.