This study demonstrated that structurally modifying sputtering-deposited ZnCr₂O₄ (ZCO) crystallites by varying the sputtering gas environment is an efficient approach to controlling the gas sensing performance of ZnO–ZCO heterostructure sensor devices. The ultra-thin ZCO films were deposited onto ZnO nanostructures to form a three-dimensional architecture. Reducing and oxidizing gas sensing measurements suggested that ZnO nanostructures coated with ZCO crystallites prepared in Ar ambient conditions exhibited superior sensitivity for the target gases. The gas sensing performance of the ZnO nanostructures coated with ZCO layers with various crystalline qualities was correlated with structural differences in the ZCO shell layers subjected to oxygen and those that were not subjected to oxygen during sputtering. The size of the interfacial depletion region at the ZnO/ZCO interface was dominated by the ZCO crystalline quality; this further influences the gas detection ability of the ZnO–ZCO heterostructures.