In eastern Indo-Gangetic Plains (EIGP), conventional rice (Oryza sativa L.)-wheat (Triticum aestivum L.) system has led to a decline in total factor productivity, input-use efficiency, and profitability. A three-year (2020–2022) field experiment was conducted at the farmers’ fields in Merha village of Katoriya, Banka, Bihar on a sandy clay loam soil to evaluate the impact of crop establishment and nutrient management on production sustainability in rice-wheat cropping system. Experiments were conducted in a split-plot design and replicated thrice. The main-plot treatment had crop establishment methods, viz. (i) Broadcasting: paddy seed broadcasted manually; (ii) Dry seeding: seed drilled on moist soil; (iii) Drum-seeding: dry-seed planted using drum seeder on moist soil and; (iv) Wet-seeding: sprouted seeds broadcasted on puddle soil with variety Sabour Ardhjal in rainy (kharif) season and 4-wheat crop establishment method, viz. (i) Broadcasting in CT; (ii) Furrow irrigated raised-bed method; (iii) ZT-drill and; (iv) Seed-cum-ferti-drill machine for wheat variety HD 2967 in winter (rabi) season. The sub-plots were allotted four nutrient management treatments, viz. (i) Farmers’ practice (130:40:10 kg NPK/ha); (ii) 100% RDF (120: 60:40 kg NPK/ha); (iii) Soil- test-based nutrient management (100% chemical fertilizer-125:75:40 kg NPK/ha) and; (iv) Soil-test based nutrient management (75% chemical fertilizer-94:56:30 kg NPK/ha+25% FYM-6.2 t/ha) in wheat, and (i) Farmers practice (140:30:10 kg NPK/ha); (ii) 100% RDF (120:60:40 kg NPK/ha); (iii) Soil-test based nutrient management (100% chemical fertilizer-150:75:40 kg NPK/ha); (iv) Soil-test based nutrient management (75% chemical fertilizer-115:56:30 kg NPK/ha+25% FYM-7 t/ha) in wheat. Our results revealed that overall system productivity and profitability were higher by 44 and 155.5% in wet seeding paddy-ZT drill wheat system in comparison to broadcasting methods of rice and wheat. System productivity was significantly higher by 28.8% in soil-test based nutrient management production system as compared to the farmers' practices. Thus, to achieve better system productivity and profitability, crops may be grown with wet seeding paddy-ZT drill wheat with soil-test based nutrient management practices under eastern Indo-Gangetic Plains of eastern India.