Interactions between plant and soil communities are known to play an integral role in shaping ecosystems. Plants influence the composition of soil communities and soil communities in turn influence plant performance. Such a plant-soil feedback may incur selection pressure on plants and the associating soil community. However, the evolutionary consequences of these above-belowground feedback interactions remain largely speculative. Here we assess whether plant-soil feedback effects differ between intraspecific plant populations and between generations within the same plant population. We used two populations of Trifolium pratense and assessed their performance when grown in association with their home versus away soil biota. Both populations were colonized by distinct microbial communities and performed better with their own home soil communities than with the soil community from the other intraspecific population, demonstrating intraspecific positive feedback effects of home soil. In one of the two populations, we found that plant performance and the root associated microbiota community differed between parental and progeny plants when inoculated with their own home soil. Differences in root associated community characteristics could explain more than 80% of the variation in performance among the progeny and parental plants. Our results highlight that intraspecific differences in both plant and associated soil communities shape plant-soil feedback effects, and consequently indicate that plant-soil feedback can influence the direction of selection between intraspecific plant populations.