Nickel (Ni) pollution in soil is a major environmental challenge to global food security necessitating its effective remediation. In this regard using plant growth promoting rhizobacteria (PGPR) and bioorganic fertilizers (BOF) to increase the effectiveness of Ni phytoextraction together with hyper-accumulator plants is an effective strategy. Thus, the aim of this study was to assess how BOF, alone or in combination with Bacillus sp. MN54 (herein after referred to as BS), promotes the growth and detoxifies Ni in Brassica juncea L. under both non-contaminated and Ni-contaminated soil conditions. The experimental design included both non-spiked and Ni-spiked soils (with two Ni concentrations: 50 and 100 mg kg−1), with the addition of BS and BOF at two different application rates (1% and 2%). Results showed that Ni negatively affected the growth attributes and yield of Brassica juncea but the integrated incorporation of BOF and BS significantly improved plant growth and physiological attributes. However, Ni stress increased antioxidant enzyme activities and triggered the production of reactive oxygen species in the plants. Likewise, the highest increases in Ni bioconcentration factor (19.9%, 72.83%, and 74.2%), Ni bioaccumulation concentration (30.6%, 327.4%, and 366.8%), and Ni translocation factor (22.2%, 82%, and 69%) were observed in soils supplemented with 2% BOF and BS under non-contaminated, 50 mg kg−1, and 100 mg kg−1 Ni-stressed conditions, respectively. The enhanced plant growth with BS and BOF under Ni stress suggested that both could efficiently promote Ni phytoextraction and simultaneously improve soil health in Ni-contaminated soil. This highlighted their potential as sustainable soil amendments for remediating Ni-contaminated soils, promoting resilient plant growth and supporting long-term ecosystem recovery.