Biocrusts play a wide range of ecological roles, especially in modifying surface soil properties and as a natural agent to combat soil degradation in fragile semi-arid and arid ecosystems globally. We examined the importance of biocrust on soil properties and quality in a semi-arid alluvial fan in northeastern Iran. The soil quality index (SQI) was used as the method for the quantitative evaluation of soil with or without biocrusts, using standard linear and nonlinear scoring methods. For this purpose, 17 biological, chemical, and physical soil properties were integrated into two indicator selection methods (total and minimum data set) and SQI has been calculated by the weighted additive method. The spatial patterns of SQI showed that overall the soil quality was (47%) increased in biocrust compared to non-biocrust soil. The increase of microbial biomass nitrogen, basal soil respiration, and microbial biomass carbon, and the decrease of available sodium and percentage sand were the most important indicators controlling the soil quality changes by biocrusts. In addition, biocrusts improved the soil structure by reducing bulk density and increasing the mean weight diameter of aggregates and available water capacity. Cyanobacteria communities of biocrusts were the initiators of soil quality improvement, while moss and cyanolichen communities played a major role from the moderate stages of biocrust occurrence. It is concluded that globally, in dry lands, biocrusts should be considered as signatures of enhanced soil quality.