Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop in the semi-arid tropics, and pod fly [Melanagromyza obtusa(Malloch)] is an important emerging constraint to increase the production and productivity of this crop under subsistence farming conditions. Host plant resistance can be used as an important tool for the management of this pest. Therefore, a set of ten pigeonpea genotypes from a diverse array of plant growth types and maturity groups including two appropriate commercial checks, was evaluated for resistance to pod fly under field conditions, and characterized for physico-chemical pod traits. The non-determinate type GP 75 (extra early maturing) and GP 118 (early maturing), and determinate type GP 233 (extra early maturing) and GP 253 (early maturing) genotypes had significantly lower pod and seed damage as compared to determinate (Prabhat) and non-determinate (Manak) early maturing checks, suggesting that resistance to pod fly is not linked to plant growth type and maturity period of the genotype in pigeonpea. Pod wall thickness, trichome density, reducing and non-reducing sugars, total phenols, tannins, and crude fiber were found to be negatively associated (r = −0.83** to −0.97**), while total protein positively associated (r = 0.88** to 0.97**) with pod fly infestation. Therefore, these traits particularly total phenols, tannins, crude fiber, trichome density, and pod wall thickness, can be used as physico-chemical markers to identify pigeonpea genotypes with resistance to M. obtusa, and use in pod fly resistant breeding program in pigeonpea.