Spring black stem and leaf spot of lucerne (alfalfa, Medicago sativa L.), caused by Phoma medicaginis, is an important disease in temperate regions of the world. It is now a serious disease threatening global lucerne production. This experiment was designed to test the combined effects of the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae and the rhizobium Sinorhizobium medicae on growth, nutrient uptake and disease severity in lucerne. The results showed that F. mosseae increased plant phosphorus and nitrogen uptake and plant dry weight, and this beneficial effect was enhanced when in association with S. medicae. Rhizobial and AM fungal effects were mutually promoting; inoculation with AM fungus significantly increased the formation of root nodules, and inoculation with rhizobium increased the percentage of root length colonised by AM fungus (P < 0.05). After infection with P. medicaginis, typical leaf spot symptoms with the lowest disease incidence and disease index occurred on plants that were host to both F. mosseae and S. medicae. Plants with both symbiotic microorganisms had higher activities (concentrations) of phenylalanine ammonia-lyase, chitinase, β-1,3-glucanase, lignin, hydroxyproline-rich glycoprotein and jasmonic acid. Therefore, the tested AM fungus (F. mosseae) and rhizobium (S. medicae) have the potential to reduce damage and yield loss in lucerne from spring black stem and leaf spot caused by P. medicaginis.