The damage caused by the southern root-knot nematode (Meloidogyne incognita) in coffee plants has been reported in various countries, including Indonesia. The measures to control the nematodes on coffee seedlings and fields depend on synthetic nematicides. Addressing this issue requires not only a more environmentally friendly and cheaper technology but also equal effectiveness comparable to synthetic nematicides. This study aimed to test the effectiveness of fortified bacterial consortium (FBC) involving a combination of liquid organic fertilizer (LOF), botanical pesticide, and a bacterial consortium to control M. incognita infection in Coffea arabica seedlings. The treatments in this study consisted of control, synthetic nematicide with the active ingredient fluopyram, and various FBC concentrations ranging from 20%, 40%, 60%, 80%, and 100%. The results demonstrated that the application of 60% to 100% FBC increased plant growth. The most effective and efficient treatment for increasing plant growth was the application of 60% FBC. When compared with control plants, 60% FBC treatment resulted in 6.8% longer root, 9.5% higher plant, 5.3% heavier plant fresh weight, and 4.8% heavier root fresh weight. We also found that the application of 60% to 100% FBC increased the amount of chlorophyll in leaves. FBC application also reduced the number of nematodes in the soil up to 60.6%, the number of galls up to 286.4%, and the severity of root damage up to 118.2%. This study indicates that the application of 60% FBC is the most effective and efficient in controlling M. incognita and stimulating the growth of C. arabica seedlings.