Ginger is an important spice crop in the north-eastern region of India. Rhizome rot, also called soft rot, is one of the most devastating diseases found in ginger that causes yield losses of up to 100% under favourable conditions. Initially, the disease symptoms appear as a light yellowing of the leaf tips that gradually spreads down to the leaf blade of lower leaves and the leaf sheath along the margin. Under favourable environmental conditions, the disease spreads rapidly, potentially causing significant crop damage. The pathogen can infect at any stage of crop growth, and under favourable environmental conditions, the disease spreads rapidly, failing the crop. Current research emphasises mitigating the losses caused by the devastating disease by using management strategies and biocontrol agents (BCAs). Results revealed that the average highest percent rhizome germination, lowest mean disease incidence, lowest mean disease severity index, lowest coefficient of disease index value, highest rhizome yield and benefit–cost ratio were recorded with Trichoderma harzianum (10 g/kg of rhizomes) + soil application of T. harzianum-enriched well-decomposed farm yard manure (3 kg of T. harzianum mixed with 100 kg FYM at 10–15 days before sowing) + soil drenching with T. harzianum at the rate 10 kg/ha, compared to the untreated control. Furthermore, soil chemical properties such as pH, electrical conductivity, soil organic carbon, total available nitrogen, total available phosphorus, and total available potassium play critical roles in rhizome rot disease severity. BCAs can suppress the phytopathogenic fungi and modulate different functions in plants.