The goal of the study was to identify the key biological indicators of soil quality under multiyear of repeated organic manuring in either rice and residual effect in wheat (System I), wheat and residual effect in rice (System II) or both rice + wheat (System III) under subtropical climatic condition. The treatments were farmyard manure (FYM), Sesbania green manure (SGM), SGM with blue green algae (BGA), SGM+FYM, SGM+FYM+ BGA in rice; Leucaena green manure (LGLM), LGLM with Azotobacter (AZB), LGLM+FYM, LGLM+FYM+AZB in wheat. The soil samples were analyzed for soil biological properties such as basal respiration (BR), microbial biomass carbon (MBC), microbial metabolic quotient (MMQ), potential mineralizable nitrogen (PMN); and soil enzymatic activities viz. dehydrogenase (DHA), fluorescein diacetate (FDA) hydrolase, acid and alkaline phosphatases (AcPA and AlkPA), arylsulfatase (ArylSA) activities. Principal Component Analysis (PCA) identified key indicators viz. AcPA, MMQ, MBC (system I), FDA, and MMQ (system II); BR, DHA, MBC (system III). Fourteen years' application of organics in system III enhanced the PMN (26 %, 43 %), FDA (31 %, 17 %), AlkPA (8 %, 9 %), AcPA (7 %, 11 %), ArylSA (36 %, 11 %) and REY (9 %, 12 %) over the system I and II, respectively. The treatment (SGM/ LGLM+FYM+ BGA/AZB) in system III triggered the soil biological quality index (SBQI), and maximized the REY (rice equivalent yield). The study proved that the application of different combination of organic manures in rice, instead of wheat, may be recommended for improvement of both SBQI and productivity of rice-wheat system in semi-arid sub-tropical region of India. The identified biological indicators can be validated and used for indexing the SBQI for monitoring the time-to-time changes in soil biological health under the changing organic management system and this finding can be implemented in and around the Indo-Gangetic plain and in larger context to south and south-east Asia having similar soil type, environmental condition and cropping systems.