Pinus ponderosa is the most planted tree species in the ecotone area of Patagonia, Argentina, subjected to water stress and a Mediterranean climate. Ectomycorrhizal (EM) fungi form obligate mutually beneficial associations with ponderosa pine which improve plant growth and resistance to adverse conditions. This work reports field results of a five-year trial aimed at determining which EM fungal species were most beneficial for pine seedling survival, growth and nutritional status after plantation. The study was conducted in two experimental plantations located in Patagonian grasslands, where ponderosa pine seedlings inoculated with Suillus luteus, Rhizopogon roseolus, Hebeloma mesophaeum and pine duff plus a control were planted in a randomized block design. Inoculation with R. roseolus and S. luteus significantly improved ponderosa pine growth following outplanting in the site subjected to higher water stress, compared with inoculations with H. mesophaeum and pine duff. Pine duff was characterized by abundant Amphinema byssoides morphotypes. These results allow recommending appropriate EM species for afforestation in vast areas of Patagonia, and confirm that different EM species behave differently after transplant, generating different plant growth that may not be detected at nursery stage. Inoculation with these growths promoting edible mycorrhizal species could provide better tree growth and a non-timber product while stands are growing.