Nowadays, zinc (Zn) fertilizers are commonly used for quality food production globally. Knowledge about proper application time and rates of commercial Zn fertilizers is necessary to obtain higher crop production and improve Zn use efficiency. A long-term field experiment was conducted during 2012 to 2018 at Anand Agricultural University, Anand (Gujarat), India, to find out the right Zn fertilizer dose and its frequency of application in maize–wheat cropping systems grown on typic haplustepts soil. The study comprised of three frequency levels, i.e., Zn application in the first year only (F1), alternate year (F2), and every year (F3), with four different rates of Zn, i.e., 2.5, 5.0, 7.5, and 10.0 kg Zn ha−1 per year imposed in the maize–wheat cropping system in each kharif season (during June to September) for six years. Findings of the study revealed that Zn applications to maize at 7.5 and 10 kg ha−1 in alternate year and 5.0 to 10 kg ha−1 in every year significantly increased maize equivalent yield as compared to no-Zn treatment. Application of 10.0 kg Zn ha−1 per year produced higher grain size, straw, and total Zn concentrations compared to those observed under no-Zn application in maize and wheat crops. Diethylene triamine penta acetic acid extractable Zn concentration in soil was higher in Zn treated plots which received Zn application at 5.0, 7.5, and 10.0 kg ha−1 in alternate years and 10 kg ha−1 in every year as compared to no-Zn application. Apparent Zn recovery efficiency varied from 0.17 to 1.46% for maize crop and 0.34 to 1.70% for wheat crop under different rates and frequencies of Zn application. The above results emphasize the importance of Zn retention capacity of soil regarding its response to different rates and frequencies of Zn application to maize and wheat crops.