Low use of chemicals in agriculture, plentiful availability of biomass and manure and favorable climatic conditions offer the opportunity for organic farming in eastern Himalayan region of India. Thus, field experiments were conducted in seven consecutive years from 2005 - 06 to 2011 -12 under a raised and sunken bed (RSB) land configuration (0.3–0.4m height, 2m width, 7m length) in lowland at Meghalaya (950m above sea level), India. The RSBs were constructed to facilitate drainage and accommodate vegetables in lowland conditions. The objectives of the study were (i) to identify suitable crops and cropping sequences for organic food production, and (ii) to assess long term impacts of organic farming on soil and produce quality. Rice (Oryza sativa L.) – vegetable sequences on raised beds and rice (varieties) – fallow (no crop) sequences on sunken beds were assessed under four farming practices in fixed plots. The four farming practices were control (only in-situ recycling of 2/3rd crop residues), organic (farmyard manure and rock phosphates), inorganic (mineral fertilizer) and integrated farming [50/50 organic and inorganic fertilizer sources (INF)]. Results indicated that seven-year average productivity of tomato (Solanum lycopersicum L.) and carrot (Daucus carota L.) under organic (22.1, and 10.1Mgha−1, respectively) and INF (21.9, and 10.4Mgha−1, respectively) were significantly higher than both inorganic (17.6, and 7.1Mgha−1, respectively) and control (3.77, and 3.1Mgha−1, respectively). However, yields of potato (Solanum tuberosum L.) and French bean (Phaseolus vulgaris L.) were the highest under INF (14.4 and 8.7Mgha−1, respectively) followed by organic (13.9 and 7.5Mgha−1, respectively). Considering farming practices, INF (3.99Mgha−1), organic (3.85Mgha−1) and inorganic (3.81Mgha−1) had the similar rice productivity in sunken beds but all had significantly higher yield than that of control. After seven years, the soil available N on raised and sunken beds under organic farming was 13.3 and 4.36% higher than that under inorganic and 20.8 and 18.2% higher than that under control, respectively. Soil microbial biomass carbon was significantly higher under organic raised (177.9μgg−1 dry soil) and sunken beds (146.77μgg−1 dry soil) than that of other farming practices. Most of the quality parameters of tomato (lycopene content, total sugar, total soluble solids) and carrot (total soluble solids, ascorbic acid, beta carotene) were superior under organic farming followed by INF. Combining all these long-term results, the study strongly suggests several benefits of organic farming for sustainable productivity and improved soil and produce quality under eastern Himalayan condition.