In recent years, interest in using encapsulated plant growth-promoting rhizobacteria (PGPR) as a biocontrol agent against root-knot nematodes has increased. Root-knot nematodes are soil-borne parasites that mostly cause annual commercial losses globally by infecting tomato plants (Solanum lycopersicum). In this work, tomato plants (cv. GS) were grown in a greenhouse to test the effectiveness of encapsulated Bacillus megaterium with or without humic acid or in liquid form at different inoculum levels against Meloidogyne javanica and their impact on different growth parameters. A scanning electron microscope (SEM) was used to visualize the microencapsulation of B. megaterium as well as viability and protease production In vitro. In a greenhouse experiment, humic acid-encapsulated B. megaterium resulted in a significant decrease in nematode parameters compared to the control group. When compared to other inoculants, the use of 10 capsules/plant decreased nematode infestation and enhanced plant growth parameters, antioxidant enzymes, and photosynthetic pigments. These results are reflected in increased dehydrogenase activity, total bacterial count, and acidic and alkaline phosphatase in soil 30 and 60 days after transplanting. Therefore, to increase the development dynamics of tomato plants and reduce nematode infestation, we advise using B. megaterium capsules supplemented with humic acid.