Rice-based production systems are critical to Nigeria's food security, but their effectiveness has decreased as soil quality deteriorates. A study was conducted on farmers' fields in Kebbi state, Nigeria to assess the long-term effects of cropping systems (rice mono-cropping (RR), rice-cowpea (RC), and rice-onion (RO)) and tillage (conventional tillage (CT) and minimum tillage (MT)) combinations on soil quality indices (SQI). The treatments were RR-CT (T1), RR-MT (T2), RC-CT (T3), RC-MT (T4), RO-CT (T5) and RO-MT (T6). Twelve soil properties that responded to management practices were measured as an unscreened total data set (TDS), and principal component analysis was performed to obtain a minimum data set (MDS). On the TDS and MDS, four SQIs were then calculated using both linear and non-linear scoring functions. Results showed that all the twelve properties varied significantly among the treatments. Treatment 3 had the lowest total nitrogen (TN) (0.31 g/kg) and the highest (0.84 g/kg), was T2. RR system with MT (T2) showed 98, 35, 95 and 138% increase in organic carbon (OC), microbial biomass C (Cmic) and N, and cation exchange capacity (CEC), respectively when compared with T3. Treatment 2 recorded the lowest bulk density (BD) (1.16 Mg/m3) and penetration resistance (0.84 MPa) after 3 years of cropping. Soil TN, CEC, OC, BD and Cmic highly influenced soil quality (SQ) explaining 85% of variation in the TDS and were selected as key indicators of SQ for the production system. All four SQIs differed significantly by treatment, with T2 showing the best strategy for sustaining the highest SQI. Equivalent rice yield (kg/ha) was positively correlated with SQI (R2 = 0.44–0.90) and had a strong relationship with TN, BD and Cmic (R2 = 0.95). The study shows that the MT could counteract any detrimental effect of monocropping in a rice-based production system.