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Sustaining soil fertility and enhancing food production on smallholder farms is a great challenge in the Indo-Gangetic plains (IGP). Soil fertility parameters viz., physical, chemical and biological, though intrinsically linked to one another in the soil environment, are often studied in isolation. This work adds value to analyses of all these three components of soil quality influenced by different cropping systems under organic and chemical farming by correlating all these parameters, otherwise left unexplored. The study compared soil physical, chemical and biological characteristics in relation to long term organic and chemical farming in a sandy loam soil. The field experiments were conducted at Punjab Agricultural University, Ludhiana, India, with two farming systems in main plots for 12 seasons and four cropping systems in sub-plots for 4 seasons. The organic farming with green manuring (GM) to basmati rice and farmyard manure to wheat in basmati rice - wheat cropping system significantly increased soil water holding capacity, mean weight diameter, soil organic carbon, cation exchange capacity, dehydrogenase activity and basal soil respiration by 42.3, 62.7, 48.9, 59.0, 55.6 and 50.3%, respectively than with chemical farming. The crop productivity was 33.9% higher in organic than chemical farming, resulting in higher net returns under GM based organic farming. Principal component analysis (PCA) distincted organic farming from the chemical farming under different cropping systems based on basal soil respiration and cation exchange capacity in PC1 (explaining 93.1% of total variability), and the carbohydrate carbon and pH in PC2 (19.5% variability). These indicators are most influential for studying soil quality under organic farming and GM based cropping systems. [ABSTRACT FROM AUTHOR]