Soil-borne plant pathogens are difficult to control, and the application of individual biocontrol agents is often limited. This limitation calls for an integrated approach, and the combination of microorganisms might result in more effective control than individual inoculations. In our study, we investigated the effects of single inoculation and coinoculation of the endophytic fungus Serendipita herbamans and the arbuscular mycorrhizal fungus (AMF) Funneliformis mosseae in protecting tomato plants from the soil-borne pathogen Fusarium oxysporum f. sp. lycopersici (Fol). We conducted two independent greenhouse experiments in which plants were grown for either eight or sixteen weeks. Plants cultivated for eight weeks received Fol chlamydospores on the day of transplanting (simultaneous Fol inoculation), whereas plants grown for sixteen weeks obtained Fol either simultaneously or two weeks later (delayed Fol inoculation). S. herbamans was inoculated via root dipping for 24 h, while AMF was applied on the day of transplanting. The disease incidence was reduced by 67% when S. herbamans was inoculated individually or by 53% when it was coinoculated with AMF in the eight-week cultivation period. Even until sixteen weeks, a reduction in disease incidence by 25% and 42%, respectively, was evident. Delayed inoculation with Fol did not affect the disease incidence, but the disease severity was increased in plants treated solely with AMF. With regard to the other parameters, the AMF partner colonized the roots readily, enhanced the phosphorus status and compensated for the growth of tomato plants challenged with Fol. In combination with the bioprotective effect mediated by the endophyte, AMF strengthened the morphological and nutritional features, providing tomato plants a long-term protective advantage when challenged with Fol.