Soil quality is a concept of many interrelated factors that perform in concert to improve soil productivity. Few of the factors for soil quality are microbial biomass, soil aggregate fractions, and carbon mineralization in different aggregate fractions that are influenced by the agricultural practices such as tillage, no-tillage, cover cropping, and compost applications. The objective of the study was to investigate the relationship between microbial biomass carbon and soil aggregates in disked and no-till systems with cover crop and compost. Four treatments include no-tillage, no-tillage with winter cover crop and compost, disk tillage, disk tillage with winter cover crop and compost. The field experimental design was randomized complete block with four replications. Carbon mineralization rates may differ among aggregate fractions because of microbial dynamics. This study tested if variations in microbial biomass among aggregate fractions influence carbon mineralization rates of soils from two tillage systems with cover cropping plus the application of compost. Soil core samples were collected at planting in June 2010 and sectioned into depths 0-7.5 cm and 7.5-15.0 cm. Samples were wet sieved and separated into fractions, oven dried and weighed. The microbial biomass carbon was determined in each aggregate fraction by fumigation method. This paper will present the microbial biomass carbon and carbon mineralization results obtained.