American ginseng (<i>Panax quinquefolius</i>) roots have long been harvested for use in herbal medicine. Overharvesting has threatened long-term viability of wild American ginseng populations. Research has been ongoing to determine factors affecting the variation of ginsenosides in roots. Given the conservation concerns regarding wild American ginseng, we began experimenting with a partial-root harvest method in 2014 for extracting tissue for ginsenoside analysis without killing individual plants or causing long-term declines in wild populations. We took partial-root harvest samples from 57 plants in four wild populations throughout western North Carolina and monitored morphological attributes of these and 56 paired, unharvested plants of similar size for four years after harvest. Partial-root samples were taken from an additional 162 plants from 16 new populations in 2015 and 2016. Morphological attributes of these plants were monitored annually or biannually. In the paired plant study, annual reemergence did not differ between harvested and unharvested plants in any year after harvest. Leaf area was significantly lower in harvested plants than unharvested controls in the first year postharvest, but these differences did not persist after the first year. In the unpaired study, preharvest-postharvest comparisons were more variable, likely due to different harvest years and interannual variation in weather. Our results demonstrate that partial-root harvest could be an effective way for ginsenoside researchers to reduce their impact on wild and cultivated American ginseng populations and it may represent a non-destructive harvest protocol for root tissue phytochemical analysis.