Soil-borne pests and pathogens, particularly root-knot nematodes (Meloidogyne spp.) and phytopathogenic fungi, are major constraints to crop productivity in the semi-arid Bundelkhand region of India. The present study evaluated the potential of indigenous bio-control agents isolated from Bundelkhand soils for the sustainable management of Meloidogyne spp. and associated fungal pathogens under laboratory, greenhouse, and field conditions. A total of 36 indigenous microbial isolates were obtained from rhizosphere soils, comprising 21 fungal and 15 bacterial isolates. Among these, Trichoderma spp. (33.3%), Pochonia chlamydosporia (13.9%), Purpureocillium lilacinum (11.1%), Bacillus spp. (22.2%), and Pseudomonas spp. (19.5%) were predominant. In vitro assays revealed that P. chlamydosporia inhibited egg hatching of Meloidogyne spp. by 78.6% and caused 65.4% juvenile mortality, while Bacillus subtilis resulted in 72.9% juvenile mortality. Dual culture tests showed maximum mycelial growth inhibition of Fusarium oxysporum (71.4%), Rhizoctonia solani (66.2%), and Macrophomina phaseolina (62.8%) by Trichoderma harzianum. Greenhouse experiments demonstrated a significant reduction in root gall index in tomato from 4.6 in untreated controls to 1.2 following application of P. chlamydosporia, along with a reduction in disease incidence from 46% to 12%. Field trials in chickpea further confirmed the efficacy of indigenous isolates, where P. chlamydosporia reduced nematode populations from 980 to 420 per 200 cc soil and increased yield from 11.4 to 16.8 q ha⁻¹. These findings validate the effectiveness of indigenous bio-control agents as eco-friendly and region-specific tools for integrated management of nematode–fungal disease complexes in Bundelkhand agriculture.