Application of boron (B) to wheat in conservation rice–wheat cropping systems may have a residual effect that improves productivity and grain quality of the following rice crop. Two field experiments were conducted to evaluate the effect of soil residual B on the performance, grain quality and grain yield of rice and soil biological properties under puddled transplanted (PuTR) and direct-seeded (DSR) rice systems on silty loam soil. A preceding wheat crop was sown using two different tillage systems, plough tillage (PTW) and no tillage (NTW), in combination with four B application treatments: control (no B), soil application (SA, 1 kg ha^–1), seed priming (0.01 M), and foliar spray (0.01 M). After wheat harvest, rice was planted in PuTR and DSR systems. The conservation tillage system in both wheat and rice (NTW–DSR) significantly increased soil organic carbon (by 18%) and soil microbial biomass carbon (by 5%) over conventional tillage systems (PTW–PuTR). Improved soil health and availability of soil residual B in the NTW-SA–DSR system improved grain yield (by 23–37%) and grain quality (grain protein by 3–8%, amylose content by 26%) over PTW–PuTR irrespective of B application method. Best economic return and net benefit were recorded in the order NTW-SA–DSR > PTW-SA–DSR > NTW-SA–PuTR. Thus, the application of B to NTW had a strong residual effect on grain quality and profitability of the following rice crop. In rice–wheat cropping systems on a silty loam soil, conservation tillage systems (NTW–DSR) significantly improved the availability of soil residual B and soil health and increased economic return.