Production of biogas through anaerobic digestion of organic wastes should play an important role in sustainable development of energy supply, and the environmental effects of digestates have to be assessed. We investigated the effect of anaerobic digestion of pig slurry (PS) on the molecular quality of the digestate produced. The consequences of digested (DPS) and undigested PS use as organic soil fertilizer on soil microbial and biochemical properties and C-gas emissions (CO2 and volatile organic compounds) were studied during a two-month incubation. PS and DPS differed in the amount of volatile organic compounds (VOCs) emitted, in their organic C and lignin contents but not in their active microbial composition. Application of both types of slurry to the soil immediately increased the content of soil dissolved organic carbon (DOC) compared to the control soil. The application of DPS induced few changes in the biochemical composition of soil organic matter compared to its raw material (PS) that increased the amount of phenolic compounds. After 60 days, both amended and control soils contained similar amounts of DOC, amended soils presenting a more diverse biochemical composition of their soil organic matter. Application of both slurries to soil triggered a succession of different active microbial communities, which could be attributed to the introduction of new microorganisms and the input of new labile organic carbon. Changes in fungal communities were stronger than those of bacteria and archaea; however, only slight differences were observed between the slurries. Different fluxes and emission dynamics of five VOCs (methanol, acetone, DMS, 2-pentanone and phenol) were observed during the incubation time following application of PS or DPS to soil while no differences in CO2 emissions were observed. The present study calls for long-term field studies with VOC analyses as a promising tool to differentiate organic fertilization practices.