Cr(VI) tolerance level of phytopathogenic fungus viz., Macrophomina phaseolina (Tassi) Goid was assessed through growth, morphological, physiological, and metal accumulation assays. Initially, the fungus growth assays indicated that the fungus can grow over concentration range of 20–3000 ppm and exhibited high tolerance index (0.88–1.00) and minimum inhibitory concentration at 3500 ppm of Cr. Observations under compound and scanning electron microscope un-revealed the structural features of hyphae under Cr stress as thick-walled, aggregated, branched, short and broken, along with attachment of irregular objects on them. Metal accumulation analysis revealed reduction in Cr(VI) accumulation by the fungus with increase in metal concentration in the growth medium (500–3000 ppm). Cr stress induced upregulation of antioxidant enzyme activities (catalase, peroxidase and polyphenol oxidase), expression of genes (MSN1 and metallothionein) and appearnace of new protein bands suggesting the possible role in protection and survival of M. phaseolina against Cr(VI)-induced oxidative stress. This study concludes that interference of Cr with growth and physiological process of M. phaseolina could affect its infection level on its host plant, therefore, synergistic action of two factors needs to be addressed, which may aid to guide future research efforts in understanding impact of plant-pathogen-heavy metal interaction.