With the aim of assessing the effects of beneficial microorganisms on greenhouse tomato “plum” grown under salinity conditions, research was carried out in southern Italy from summer to winter, by comparing two arbuscular mycorrhizal fungi (AMF) based formulates (Rizotech Plus, Myco Apply DR) and a non-inoculated control, in factorial combination with four soil electrical conductivities (1.5, 3.0, 4.5, 6.0 mS·cm−1 EC). The highest root colonization was 83% at 3.0 mS·cm−1 under AMF-based treatments and 34% at 1.5 mS·cm−1 in non-treated control; the latter attained lower values than AMF treatments at any soil EC. Harvest occurred 3.5 days earlier in control plants, six days earlier under 6.0 mS·cm−1 EC compared to 1.5 mS·cm−1. The inoculated plants always showed higher yield than the control ones and the highest production at 4.5 mS·cm−1 EC; control plants attained the highest yield under 3.0–4.5 mS·cm−1 EC. The highest values of most fruit quality indicators, mineral elements and antioxidant compounds and activity were recorded under AMF-based formulates inoculation and 6.0 mS·cm−1 soil EC. Beneficial microorganisms proved to be an effective environmentally friendly tool for improving tomato yield and quality performances in both normal and soil salinity conditions.