A research trial was conducted at Agronomy Farm (SKUAST-K, Wadura, Jammu & Kashmir), during kharif 2017 and 2018 to evaluate nutrient removal in rice under various rice establishment methods and weed control measures. The study comprised of two factors: rice establishment techniques {Transplanting (TPR); Direct seeding (DSR) and System of rice intensification (SRI)} as main plot treatments and weed control measures {Butachlor @ 1500 g a.i ha−1 (B); Penoxsulam @ 22.5 g a.i ha−1 (P); Pyrazosulfuron ethyl + Pretilachlor @ 15 and 600 g a.i ha−1 (PP); Bensulfuron methyl + Pretilachlor @ 60 and 600 g a.i ha−1 (BP); 2 Conoweeding/Hand Weeding (CW/HW); Weed free (WF) and weedy check (WC)} as sub-plot treatments meant to evaluate the best establishment method and weed management practice for rice. Over DSR and transplanted rice, the SRI technique yielded a significant increase in dry biomass accumulation (17.04 and 17.20 t ha−1) and grain (7.92 and 8.17 t ha−1) and straw (9.60 and 10.17 t ha−1) yields. Penoxsulam herbicide significantly showed higher grain and straw yield of 8.19 and 8.28 t ha−1 and 10.13 and 10.44 t ha−1, respectively, than other weed management measures by comparing the means using critical difference. TPR excelled in reducing dry weed biomass more than other established methods. All herbicides considerably reduced dry weed biomass, but Penoxsulam herbicide showed the greatest reduction in dry weed biomass and proved superior against complex weed flora. Weeds showed maximum contribution towards total Biomass under DSR, among rice establishment techniques. In contrast, among different weed control measures, it was maximum in weedy check treatment (Untreated Control) and minimum in penoxsulam treatment. SRI significantly excelled in crop (grain and straw) nutrient uptake compared to the DSR and TPR method, although different crop establishment techniques non-significantly influenced nutrient concentrations. Furthermore, penoxsulam treatment demonstrated higher crop (grain and straw) nutrient uptake among the various weed management measures. However, available soil nutrients were observed among establishment techniques, highest in DSR and lowest in SRI. Moreover, direct-seeded rice excelled SRI and transplanted rice in weed nutrient uptake, and among the different herbicidal treatments, penoxsulam recorded the lowest uptake in weeds. Nutrient budgeting demonstrated that DSR showed the maximum percentage of nutrient removal by weeds, and the minimum ratio was in TPR. In contrast, the lowest rate of nutrients removed via weeds were seen in penoxsulam application under various weed management measures.