Appropriate land configuration and assured nutrient supply are prerequisites for quality organic baby corn (Zea mays L.) production in high rainfall areas of the delicate Eastern Himalayan Region of India. A long term (5-year) study was conducted during 2012-2016 on a sandy loam soil in the mid attitude of Sikkim, Eastern Himalayan Region of India to evaluate the productivity, produce quality, the profitability of baby corn, and soil properties under different land configurations comprising flatbed, ridge and furrow, and broad bed and furrow, and organic nutrient management practices comprising un-amended control, farmyard manure 12 t ha-1, vermicompost 4 t ha-1 and farmyard manure 6 t ha-1 + vermicompost 2 t ha-1. The baby corn sown on broad bed and furrow had the tallest plant (149.25 cm), maximum dry matter (64.33 g plant-1), highest leaf area index (3.5), maximum cob length (8.10 cm), cob girth (6.13 cm) and cob weight (8.14 g) leading to significantly higher fresh baby corn yield (1.89 t ha-1), and net returns (US$ 906.1 ha-1) than those of other treatments. Mineral composition (phosphorus, potassium, iron, and zinc), protein, and ascorbic acid content were also the highest in baby corn grown under the broad bed and furrow system. The soil of broad bed and furrow had a higher pH, organic carbon content, organic carbon pools, microbial biomass carbon, and enzymatic activities (dehydrogenase, fluorescein diacetate, and acid phosphatase) compared to soils of other land configurations. A combined application of farmyard manure (6 t ha-1) + vermicompost (2 t ha-1) improved the crop growth and produced 117.8% higher fresh baby corn and 99.7% higher fodder yield over control (0.9 t fresh corn and 13.02 t fodder yield ha-1), respectively. This treatment also registered significantly higher gross return (US$ 1746.9 ha-1), net return (US$ 935.8 ha-1), and benefit-cost ratio (2.15) than other nutrient management practices. Fresh cob quality in terms of protein (22.91%) and ascorbic acid content (101.6 mg 100 g-1) was observed to be significantly superior under combined application of farmyard manure (6 t ha-1) + vermicompost (2 t ha-1) than those of other nutrient management systems. However, fresh baby corn cobs produced with vermicompost 4 t ha-1 had the highest concentration of phosphorus, potassium, iron, and zinc. Application of farmyard manure 12 t ha-1 registered the maximum increment in soil organic carbon content (1.52%), its pool (40.6 t ha-1) and carbon sequestration rate (0.74 t ha-1 year-1) followed by integrated application of farmyard manure (6 t ha-1) and vermicompost (2 t ha-1). The maximum soil microbial biomass carbon and enzymatic activities [dehydrogenase (22.1 µg TPF g-1 soil h-1) and fluorescein diacetate (67.1 µg FDA g-1 soil h-1)] were noted with the combined use of farmyard manure (6 t ha-1) + vermicompost (2 t ha-1). Thus, the study suggests that the broad bed and furrow land configuration along with the combined application of farmyard manure + vermicompost could be an economically feasible practice for quality organic baby corn production and soil health improvement in the Eastern Himalaya and other similar eco-regions elsewhere.