The hill ecosystem of Northeastern Himalayas is suitable for organic farming due to negligible use of fertilizer (<12 kg ha−1) and agrochemicals, abundance of organic manure, especially plant biomass, and favourable climatic conditions for diverse crops. For successful organic farming, efficient cropping systems and organic amendments are to be identified to sustain soil health on one hand and productivity and enhanced income on the other. The efficacy of three organic amendments, namely, farmyard manure (FYM), vermicompost (VC) and integrated nutrient source (INS; 50% recommended dose of nitrogen (N) through FYM + 50% N through VC) on performance of three-vegetable-based cropping systems, namely, maize + soybean (2:2 intercropping)–tomato, maize + soybean–potato and maize + soybean–French bean was evaluated for five consecutive years (2005–06 to 2009–10) under subtropical climate at Umiam, Meghalaya, India (950 m above sea level). All the organic amendments were applied on N equivalent basis and phosphorus (P) requirement was compensated through rock phosphate. The results revealed that the yield of vegetables, except root vegetables, was maximum with FYM as soil amendment. Total system productivity in terms of maize equivalent yield (MEY) was significantly higher under FYM followed by INS. Pooled analysis revealed that MEY was enhanced by 200 and 191% with continuous application of FYM and INS, respectively, over control (no manure). Maize + soybean–tomato system recorded the highest MEY (28.78 Mg ha−1; Mg – megagram) followed by maize + soybean–French bean (24.37 Mg ha−1). INS as organic amendment resulted in maximum improvement in soil organic carbon (SOC), available P and potassium (K), soil microbial biomass carbon and water holding capacity and was similar to those under FYM. The SOC concentration under INS (23.6 g kg−1), FYM (23.3 g kg−1) and VC (22.3 g kg−1) after five years of organic farming were 31.0, 29.4 and 23.8% higher than the initial and 26.2, 24.6 and 19.3% higher than those under control, respectively. The quality traits of tomato such as total soluble solids (5%), ascorbic acid (28.6 mg 100 g−1) and lycopene content (19.35 mg 100 g−1) were higher under FYM application than other amendments. The study indicated that FYM and INS are equally good as organic amendment and their continuous application not only improves soil health but also crop productivity. FYM application was also found to be cost effective as it resulted in a higher benefit: cost ratio (4.4:1) compared to other amendments irrespective of cropping sequences during transition to organic farming.