The objective of this work was to identify soil parameters potentially useful to monitor soil quality under different soil management and crop rotation systems. Microbiological and chemical parameters were evaluated in a field experiment in the State of Parana, southern Brazil, in response to soil management [no-tillage (NT) and conventional tillage (CT)] and crop rotation [including grain (soybean, S; maize, M; wheat, W) and legume (lupin, L.) and non-legume (oat, O) covers] systems. Three crop rotation systems were evaluated: (1) (O/M/O/S/W/S/L/M/O/S), (2) (O/S/L/M/O/S/W/S/L/M), and (3) (O/S/W/S/L/M/O/M/W/M), and soil parameters were monitored after the fifth year. Before ploughing, CO 2-emission rates were similar in NT and CT soils, but plough increased it by an average of 57%. Carbon dioxide emission was 13% higher with lupin residues than with wheat straw; decomposition rates were rapid with both soil management systems. Amounts of microbial biomass carbon and nitrogen (MB-C and MB-N, respectively) were 80 and 104% higher in NT than in CT, respectively; however, in general these parameters were not affected by crop rotation. Efficiency of the microbial community was significantly higher in NT: metabolic quotient ( qCO 2) was 55% lower than in CT. Soluble C and N levels were 37 and 24% greater in NT than in CT, respectively, with no effects of crop rotation. Furthermore, ratios of soluble C and N contents to MB-C and MB-N were consistently lower in NT, indicating higher immobilization of C and N per unit of MB. The decrease in qCO 2 and the increase in MB-C under NT allowed enhancements in soil C stocks, such that in the 0-40 cm profile, a gain of 2500 kg of C ha -1 was observed in relation to CT. Carbon stocks also varied with crop rotation, with net changes at 0-40 cm of 726, 1167 and -394 kg C ha -1 year, in rotations 1, 2 and 3, respectively. Similar results were obtained for the N stocks, with 410 kg N ha -1 gained in NT, while crop rotations 1, 2 and 3 accumulated 71, 137 and 37 kg of N ha -1 year -1, respectively. On average, microbial biomass corresponded to 2.4 and 1.7% of the total soil C, and 5.2 and 3.2% of the N in NT and CT systems, respectively. Soil management was the main factor affecting soil C and N levels, but enhancement also resulted from the ratios of legumes and non-legumes in the rotations. The results emphasize the importance of microorganisms as reservoirs of C and N in tropical soils. Furthermore, the parameters associated with microbiological activity were more responsive to soil management and crop rotation effects than were total stocks of C and N, demonstrating their usefulness as indicators of soil quality in the tropics.