Iron (Fe) is a crucial nutrient for plant growth (e.g. chlorophyll production), and though it is one of the most abundant elements in soil, very low bioavailability can limit plant growth. Studies indicate that many soil bacteria and fungi (e.g. mycorrhizal) play a role in Fe nutrient cycling and plant production, but the evidence for fungal support of plant growth is overwhelmingly correlative and in need of experimental corroboration. An Andean native potato landrace was grown in a greenhouse under Fe limitation and using three levels (Low, Medium, High) of foliar fertilization (FeEDDHA). Application occurred at 45, 60 and 70 days of growth corresponding to periods where Fe limitation is expected to be greatest. The rhizosphere soils were sampled at the flowering stage (80 days). Soil bacterial and fungal communities were examined using high-throughput sequencing of 16S and ITS regions of ribosomal RNA gene, respectively, followed by analysis using Quantitative Insights Into Microbial Ecology (QIIME v1.8). Multivariate data analyses showed that Fe fertilization of leaves significantly (p < 0.05) influenced the beta diversity of fungi but not bacterial communities in the rhizosphere. Using our novel approach, it was expected and confirmed that fungal communities would shift and mycorrhizal genera (Glomus) would be altered, however, the degree to which community change was observed was more than expected. Glomeromycota (∼16.3%) related to the family Gigasporaceae accounted for 2.8% of OTU and were 2–3 times greater in the rhizosphere of high relative to medium and low Fe conditions. Overall, the results indicate that foliar addition of Fe influences plant Fe and resonates into the root system to affect rhizosphere fungal communities. Potato Fe status thus appears to impact potato root-fungal interactions potentially mediated through mycorrhizal fungi.