Although the application of organic amendments to arable soils is considered to be a suitable tool for improving soil fertility and enhancing carbon (C) stocks, more research is required on the influence of input of organic matter on the activity and structure of the soil’s microbial community. The aim of this work was therefore to make a comparative study of the effects of organic materials with different degrees of stabilization and source (an untreated pig slurry, the solid fraction of the digestate from the anaerobic fermentation of pig wastes, a livestock-derived organic matter compost, and an urban waste compost) on the size, activity, and structure of the microbial community in two arable soils. These effects, studied through a laboratory incubation experiment, were related to the quantity and quality of organic matter added, as well as to the rapid changes in the more labile water-soluble organic matter fraction. Particular attention was devoted to the short-term variations after organic amendment, during which changes in CO2 emissions, microbial biomass C, and water-extractable organic C pools were most pronounced. Phospholipid fatty acid profiles and 16S rDNA sequence analyses evidenced changes in the microbial community structure of amended soils. Modifications of the structure of bacterial communities after amendment, generally involving declining proportions of Gram-positive bacteria (Actinobacteria and Firmicutes) and an increase in abundance of Gram-negative bacteria (Acidobacteria, Bacteriodetes, and Proteobacteria), were both quality and quantity dependent, with effects being proportional to the mineralizable organic C content of the added materials.