Tropical soils are highly-weathered acidic soils and frequently present two intersecting problems that can be detrimental to plant development: low phosphorus (P) and high manganese (Mn) availability. Mn can be phytotoxic, damaging the photosynthetic apparatus and/or competing with other nutrients. Eucalyptus grandis is often cultivated in such soil types and, despite being a tree generally tolerant to Mn excess, P deficiency may exacerbate toxicity. Arbuscular mycorrhizal (AM) fungi are known for their ability to provide P to the host plant in exchange of photosynthates. This symbiosis may also decrease Mn accumulation and overall alleviate metal stress. In a glasshouse experiment, E. grandis plants were grown for seven months in soil with low P availability adjusted to three Mn dose levels (control, 75 and 150 mg kg–1), with (AM) or without (NM) inoculation with Rhizophagus irregularis. We measured biomass, height, flavonoids (anthocyanin/flavonol) and chlorophyll indexes, chlorophyll a fluorescence parameters, AM colonization and Mn, P, Mg, K and Fe concentrations in shoots and roots. All plants presented low biomass production, and shoot P concentrations ranged from 0.13 to 0.52 g kg–1. Mn additions decreased mycorrhizal colonization, but no other negative impacts were seen in E. grandis, indicating that this species is relatively tolerant to excess Mn. At dose 75, shoots accumulated up to 2,000 mg Mn kg–1; however, this amount was not detrimental to most parameters, especially in NM plants, which had higher growth and Mg concentrations while presenting much lower flavonol and anthocyanin contents. At dose 150, plant Mn concentrations were similar to those at 75 Mn, despite higher soil availability, indicating that shoot concentrations around 2,000 mg kg–1 were a threshold for E. grandis under P deficiency. AM colonization intensity and arbuscule abundance were overall low, resulting in no improvements in P nutrition nor reduction of Mn uptake in high Mn treatments. However, AM symbiosis led to higher chlorophyll contents and non-photochemical quenching values, which are important in withstanding abiotic stress. Even though AM fungi inoculation did not improve P uptake, multivariate analysis suggests that the mycorrhizal pathway influenced nutrient acquisition in AM plants. Our results show that in E. grandis Mn excess had an alleviation and a hormetic effect, mitigating P deficiency stress rather than being phytotoxic. AM symbiosis did not improve mineral nutrition, despite providing some benefits involved in stress tolerance.