Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea ( Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F2:3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% ( CaqFe3.4 ) to 13.4% ( CaqFe4.2 ). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% ( CaqZn8.1 ) and 13.7% ( CaqZn4.3 ). Three QTLs for seed Fe and Zn concentrations ( CaqFe4.4, CaqFe4.5 , and CaqZn4.1 ) were colocated in the “ QTL-hotspot ” region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties.