In the present study, biocontrol potential of Bacillus subtilis CRB7 was evaluated to counter root-knot nematode infestation in tomato grown under protected cultivation. Under pot conditions, gall formation on roots was reduced when B. subtilis CRB7 applied at 1.25, 2.5 and 5 g plant−1. Nursery drench with B. subtilis CRB7 at 5, 10 and 15 g m−2 significantly reduced gall formation on roots (37.0 to 85.8%). Further, application of B. subtilis CRB7 as nursery drench at 15 g m−2, soil drench at 0.5% at 30 day’s interval and soil application of enriched vermicompost (5 kg 2 tonnes−1 of vermicompost ha−1) significantly reduced gall formation on roots (58.3% and 54.2%) and enhanced yield (29.8% and 15.4%) in two consecutive protected field experiments, respectively. Given its potent efficacy, B. subtilis CRB7 emerges as a promising component for the management of root-knot nematode in tomato grown under protected cultivation.