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Determining the best conservation agriculture practices for increasing soil organic carbon (C) and hence soil quality is of paramount importance in the semi-arid Mediterranean environment, where soils are experiencing a continuous decline in organic matter. Therefore, the aim of this long-term study was to assess the combined effects of tillage system and crop sequence on soil organic C and biochemical properties of soil generally used as indicators of soil quality. After 23 years of continuous application of contrasting tillage systems (conventional tillage [CT], vs. no tillage [NT]) and crop sequences (wheat monoculture vs. wheat-faba bean rotation), soil samples were collected from topsoil (0–15 cm) and subsoil (15–30 cm) at three different times during a cropping year. Soil samples were analyzed for total and labile organic C pools, microbial biomass C (MBC) and microbial biomass N, basal respiration, and the abundance of main microbial groups by phospholipid fatty acids. Long-term NT increased total organic C (TOC) at a yearly rate of 0.17 g kg−1. This in turn stimulated microbial biomass, in particular Gram-negative bacteria. This suggests a higher soil quality in NT, as was confirmed by the increase in MBC/TOC and the decrease in stress indices. In contrast, no differences were observed with regard to fungal biomass. These findings suggest the need to reconsider the role of specific bacterial groups in organic C accumulation in soils of semiarid environments. It is interesting that the effects of long-term NT varied widely by crop sequence, whereas in CT changes in biochemical characteristics and in the main microbial groups due to crop sequence were modest. Thus, the interaction among various aspects of agronomic management modulates the effects of substrate quality on chemical and biological properties of soil.