Cotton–wheat (CW) is an important cropping system in South Asia. Wheat yields under a conventional CW system are generally lower compared to a rice–wheat system due to delayed seeding. Relay seeding of wheat can help timely sowing, capturing residual soil moisture of last irrigation to cotton, and increase the productivity and profitability of CW system. The field experiment included two Bt-cotton genotypes having different canopy cover (RCH 776 and MRC 7017), two types of relay seeders (RSs) for cotton planted at 67.5-cm and 101-cm row spacing and four types of relay seeding methods (manual broadcast, strip rotor (SR) and zero-till double disc and conventional till). Relay planting of wheat allowed one additional boll picking, which increased seed cotton yield by 12% compared with conventional tillage wheat. Cotton genotypes and RSs had no effect on emergence and yield of wheat. The RSs with SR and zero till double disc furrow openers performed better in terms of wheat emergence and grain yield compared to zero-till tine openers. Under relay seeding, wheat sowing was advanced by 31 days, which increased grain yield by 18.8% compared with conventional tillage practice. Net returns from the CW system with relay seeding of wheat were higher by US$ 311 to 425 ha−1 compared with the conventional CW system.