Crop productivity and yield are adversely affected by abiotic and biotic stresses. Therefore, finding out the genes responsible for stress tolerance is a significant stride towards crop improvement. A gene co-expression network is a powerful tool to detect the most connected genes during heavy metal (HM) stress in plants. The most connected genes may be responsible for HM tolerance by altering the different metabolic pathways during the biotic and abiotic stress. In the same line we have performed the GSE86807 microarray analysis of chickpea during exposure to chromium, cadmium and arsenic and analyzed the data. Common differentially expressed genes (DEGs) during exposure to chromium, cadmium and arsenic were identified and a co-expression network study was carried out. Hub and bottleneck genes were explored on the basis of degree and betweenness centrality, respectively. A gene set enrichment analysis study revealed that genes like haloacid dehydrogenase, cinnamoyl CoA reductase, F-box protein, GDSL esterase lipase, cellulose synthase, β-glucosidase 13 and isoflavone hydroxylase are significantly enriched and regulate the different pathways like riboflavin metabolism, phenyl propanoid biosynthesis, amino acid biosynthesis, isoflavonoid biosynthesis and indole alkaloid biosynthesis.