Evaluation of the ecological sustainability of different cropping systems is crucial to achieve sustainable agriculture. This evaluation is accessible via soil quality assessment. Therefore, to study the mid-term effects of different conservation tillage systems (no tillage and minimum tillage) and cover cropping on the biological indicators of soil quality, a factorial experiment in a completely randomized block design was conducted in Dastjerd region (Hamedan). Three levels of tillage (NT: no tillage, MT: minimum tillage and CT: conventional tillage) and two levels of cover cropping (C1: Lathyrus sativus and C2: no cover crop) were applied for four consecutive years. Soil sampling was performed in the fourth year of experiment in two steps (1- before cover crop plantation, and 2- after harvesting main crop) with three replications. Most indices (total organic carbon, active carbon, basal respiration, phosphatase activity) were significantly affected by cover crop, tillage systems and sampling time, as the highest values were obtained in NT-C1 in time 2 and the lowest ones in CT-C2 in time 1. For instance, after four years application of treatments, the mean active carbon content was increased from 927 mg/kg in the conventional tillage + no cover crop to 1350 mg/kg in the conservation tillage systems + cover crop. Therefore, conservation tillage practices combined with Lathyrus sativus cover crop were shown to be the most appropriate management for soil quality maintenance and improvement.