Agriculture faces growing population pressure for food security and sustainability. Controlling root-knot nematodes and reducing fertilizer use is crucial for environmental resources preservation. In Egypt, tomato production faces pollution and human health risks by using chemical nematicides to control this nematode. So, PGPRs can improve crop productivity by controlling parasitic nematodes and biofertilization. This experiment was established to study the role of bacterial strains for controlling root-knot nematode, Meloidogyne incognita and saving nitrogen fertilizer in a greenhouse naturally infested nematodes and cultivated by tomato plants. Tomato plants were exposed to foliar spraying and soil drenching of different bacterial strains (fusant F7, Bacillus thuringiensis (Bt), Bacillus cereus (Bc) and Achromobacter xylosoxidans (Ax) compared to chemical nematicide (Oxamyl) for controlling root-knot nematode, M. incognita and saving nitrogen fertilizer (Nitrogen treatments: 30 and 60 N for greenhouse). The modified fusant F7 and its parental strains on M. incognita's nematode reproduction using spraying foliage and soil drench methods. Results showed that all treatments effectively reduced root-knot nematode reproduction, with fusant F7 being more effective in reducing soil parameters like J2, galls, and egg masses. Soil drench achieved the best reduction compared to spraying foliage. Amplification of the protease gene which is reasonable for nematode control from strains Bc and Bt, as well as fusant F7, produced 1100 base pair fragments, confirming gene presence. Results clearly reported that biofertilizer treatments significantly improved all vegetative growth (plant length, number of branches per plant, number of leaves per plant, fresh weights of leaves per plant and dry weights of leaves per plant), flowering and fruit yield (number of clusters per plant, number of fruits per plant, fruit yield) and tomato fruit quality characteristics (average fruit weight, fruit diameter and TSS%) grown under deficit nitrogen treatment. Tomato plants which received the minimum quantity of nitrogen fertilizers (30 N/greenhouse) and treated by fusant F7 as a soil drench produced the highest significant values of vegetative growth, flowering and fruit yield and fruit quality of tomatoes characteristics. SDS-PAGE protein banding patterns to 11 leaves tomato plant treatments varieties for leaf water soluble proteins. The proteins extracted migrated in the 24–191kDa range. In comparison to lesser number 7 bands in the control, the plant exposed to F7 in soil drench spraying showed a highest number of bands (17 bands).