Mutualisms between plants and microbes can have profound impact on the fitness of both partners. In these relationships, the fitness of the plant is shaped by the plant’s genetic influence on traits as well as the genetic influence of the partner. The impacted traits are not limited to only those involved in the mutualism but also includes other functional traits. In the legume-rhizobia symbiosis, plants acquire their symbionts through horizontal transmission and are unaware of their nitrogen fixation ability (partner quality) prior to nodulation. Since rhizobia may be unevenly distributed within a local patch, this can lead to the host population experiencing significant variation of trait phenotypes. We set up a single-strain inoculation study where Trifolium barbigerum was exposed to 77 strains to characterize how strength and patterns of phenotypic selection varies depending on the quality of the microbial partner. We also assess whether there is overall fitness alignment between host plant and symbiont and if there may be conflicts over optimal trait values.