Recent studies have shown that microbial polysaccharides and cellular constituents (proteins, amino acids, peptides, chitin) have a longer residence time in soil than lignin, and are preferentially stabilized as soil organic matter (SOM) over the long-term. These studies suggest that carbon first passes through the microbial pool before being stabilized as SOM. This study aims to elucidate the link between organic residue (OR) quality, N amendments, and the function of microbial communities in SOM stabilization. This was achieved in a medium-term (200 days) incubation experiment through the integration of microbial methods designed to target different physiological aspects of the microbial community: growth yield efficiency (GYE), extracellular enzyme activity, respiration, PLFA and the measurement of SOM quantity at five time points along the decomposition continuum. Microbial GYE was found to decrease with increasing respiration, suggesting a decrease in GYE with increasing availability/lability of the substrate. After 15 days of incubation, the addition of mineral N increased GYE for low quality residues (Maize, Tithonia stems) and decreased GYE for high quality residues (Tithonia (leaves+stems), Tithonia leaves). The N effect could no longer be detected by day 65. A similar effect was observed with enzyme activity. Respiration was positively correlated with the mean weight diameter (MWD) of the soil. The increase in MWD with increasing respiration illustrates improved aggregation as a result of microbial activity. The impact of residue quality and N amendment on aggregation, however, decreases with time. An increased understanding of the role that microorganisms play in organic residue decomposition and SOM stabilization will help to improve predictive soil organic carbon models by considering microbial responses to agricultural management practices.