Fusarium tomato wilt is one of the most prevalent and damaging diseases wherever tomatoes are grown intensively. Progress in agriculture in the twenty-first century is set to be based on lowering agrochemical inputs (implementation of Directive 2009/128/EC on sustainable use of pesticides), which can be achieved to some extent through the use of beneficial microorganisms. This study aimed at comparing the effects of the mycorrhizal fungus Rhizophagus irregularis and the biological control agent Trichoderma asperellum strain T34 on the incidence of fusarium wilt and the growth of tomato plants. Both R. irregularis and T34 lowered disease incidence at similar rates, compared to control plants. R. irregularis added below the seedlings reduced disease incidence more than when it was mixed with the substrate. T34 and R. irregularis increased plant height to the same extent, compared to both control and diseased plants. R. irregularis gave the highest levels of chlorophyll, followed by T34 and control plants; however, the measures for infected plants were slightly better for T34 than for R. irregularis. T34 and R. irregularis had similar effects on Ca, Mg, S, Mn, B and Si uptake in tomato plants, but R. irregularis induced a greater P, K, Zn, Cu and Mo accumulation than T34. Interestingly, at the end of the experiment, the depletion of the substrate was lower on Ca, Mg and S for plants inoculated with either R. irregularis or T34 compared to control plants, while the substrate for T34-treated plants had the lowest levels of Fe, Mn, Zn and Cu.