Indian mustard (Brassica juncea L. Czern. & Coss.) is a major oilseed crop whose productivity is severely constrained by fungal, bacterial, and viral diseases, notably Alternaria blight, Sclerotinia stem rot, white rust, and Turnip mosaic virus, causing yield losses of up to 60% under favourable conditions. Dependence on chemical pesticides for disease control has resulted in environmental contamination, resistance development, and residue-related concerns, underscoring the need for sustainable alternatives. Biological control using beneficial microorganisms such as Trichoderma, Bacillus, Pseudomonas, and Streptomyces has shown considerable potential in suppressing mustard pathogens through competition, antibiosis, mycoparasitism, lytic enzyme production, and induction of systemic resistance. Field-level application of these agents via seed treatment, soil application, root dipping, and foliar sprays has consistently reduced disease severity and improved crop performance. In parallel, host plant resistance provides a durable management option, with resistant or tolerant genotypes including Pusa Bold, RH-749, NRCDR-2, RH-406, and Giriraj, and resistance genes such as Rcr1, LepR1–LepR3, and BjuWRR1 contributing to enhanced disease resilience. Integrating resistant germplasm with compatible microbial biocontrol agents offers synergistic and stable disease suppression, reduces reliance on chemical fungicides, and supports climate-resilient, eco-friendly mustard production across diverse agro-ecological regions.