Micronutrients deficiency particularly zinc (Zn) and boron (B), and some sustainability issues, in the conventional rice-wheat cropping systems (RWCS), are threatening the performance and productivity of this important system. Experiments were conducted at farmer field in Punjab, Pakistan to improve the productivity of conventional and conservation RWCS through Zn and B application. Residual effect of both Zn and B on the following rice and wheat both crops were also investigated. In the experiments first and second, wheat was grown under zero tillage (ZT) and conventional tillage (CT). In first experiment, Zn was applied as was delivered as foliar application (FA; 0.025 M), soil application (SA; 10 kg ha-1) and seed priming (SP; 0.5 M); while in experiment second, B was applied as SP and FA (0.01 M) and SA (1 kg ha-1). After the wheat harvest, rice was seeded in puddled-transplanted (PuTR) and direct seeded aerobic (DSAR) conditions. In the experiments third and fourth, rice was planted under PuTR and DSAR; and Zn was applied in third experiment as SA (10 kg ha-1), SP (0.01 M) and FA (10 kg ha-1). Whereas, in experiment fourth, B was delivered as SP (0.01 M), FA (0.25 M) and SA (1 kg ha-1). After the rice harvest, wheat was seeded in CT and ZT. Experiments were executed in randomized complete block design in split-plot arrangements and replicated four times. Conventional and conservation tillage in both rice and wheat significantly affected the soil health, weeds dynamics and grain yield. Soil physio-biological properties were better in zero till wheat (ZTW) than plough till wheat (PTW) evident from high soil organic matter (OM), soil organic matter (SOC) and microbial biomass nitrogen (MBN). Moreover, PTW-PuTR system had poor soil health and fertility than ZTW-DSAR. In first experiment, the ZTW yield was higher than PTW; Zn, SP in ZT improve grain yield 40% and 32.3% during first and second year, respectively. Grain Zn concentration increases by 38-58% with SA and FA, Zn. Residual effect of Zn on following rice crop improve grain yield by 19% in rice followed PTW-SA and ZTW-SA; and grain Zn concentration increased by 29% in rice followed ZTW-SA. In second experiment, B, SP in ZTW and SA in PTW increase 30.52% and 30.29% during first year; whereas 25-28% during second year, respectively. SA, FA, B increased grain B from 20-35% during both years; residual B increase rice grain yield by 36% in the ZTW-SA and PuTR-SA and grain B concentration by 30% in rice followed ZTW. In experiment 3, DSAR produced 21% and 24% higher yield than PuTR with SP and SA, Zn and grain Zn concentration increased by 57% with SA, Zn. Residual Zn effect on Zn increase grain yield by 40% in wheat followed by DSAR-SA; ZTW yield was 4.85% higher than PTW. In fourth experiment, DSAR produced higher yield than PuTR; moreover, SP and SA, Zn improved 34% and 28% respectively. Residual effect of B improved grain yield in ZTW followed by DSAR-SA by 15% and grain B concentration by 25% in wheat followed the DSAR-SA. The PuTR-PTW had poor soil structure due to highest soil bulk density, lowest soil porosity, the low OM, the SOC and MBN than DSAR-ZTW. In conclusion, switching from conventional to conservation tillage systems improved the profitability, productivity and soil health under the RWCS. Application of Zn and B and their carry over effect on following crops greatly contributed to enhance performance of rice and wheat under conservation tillage systems.