Agricultural soils are important C reservoirs that influence global climate change. Plants modulate the soil environment by reduced C release from their roots or through rapid nutrient uptake from the soil by their related microorganisms. Microbial metabolic functions (catabolic and anabolic) are essential control valves for soil organic matter (SOM) turnover and also an essential factor in increasing agricultural soil productivity and decelerated increase in atmospheric CO2 concentration. However, studies on C and nutrient cycling mostly focus on the effect of organic matter input but rarely combined with their microbial metabolic processes (catabolic and anabolic pathways) in SOM turnover. In this thesis, I have investigated the microbial metabolic processes involved in organic matter decomposition, transformation, and accumulation in agricultural soils, depending on the impact of substrate-nutrient stoichiometry ratios (such as C/N ratios) of organic compounds and the type of organic matter (such as labile root exudates and lignin). This overarching research goal has been explored in three different experiments.In the first experiment, I investigated the effect of different C/N ratios with low molecular weight and labile plant-derived organic matter (such as root exudates) on microbial activities. I incubated a paddy field soil with three artificial root exudates characterized by different C/N ratios (CN6, CN10, and CN80) using a mixture of glucose, oxalic acid, and alanine. In the second experiment, I focused on the microbial degradation of a complex plant biomacromolecule (lignin), which is considered stable particularly under anaerobic conditions. I incubated the soil for 365 days to investigate the microbial degradation of lignin (13C lignin >98 atom%, 80% chemical purity) under anaerobic, followed by aerobic, conditions at different time intervals. While the first two studies dealt with short- and intermediate-term incubation experiments, in a third experiment, I focused on soil samples collected from the field along with from a large-scale area from three primary crops (maize, wheat, and paddy) to investigate the bioavailability of soil organic C (SOC), total N (TN), and organic P concentration in agricultural soils.In the first experiment, root exudates with low C/N ratios (such as CN6 with high N content) had 2.3-fold higher CO2 emissions than those with high C/N ratios (such as CN80 with low N content) after 45 days incubation. An associated increased C- to N-hydrolase ratio with increasing substrate C/N ratio suggests that the C/N stoichiometry of root exudates controls SOM mineralization by affecting the specific microbial response through the catabolic activity of C- and N-releasing extracellular enzymes to adjust the microbial C/N ratio. The high C use efficiency (CUE) corresponded to a high C/N ratio of root exudates, indicating that low N-containing root exudates increased the CUE for their biomass synthesis for C accumulation. In the second experiment, the microorganisms degraded lignin under anaerobic and aerobic conditions as indicated by the cumulative CO2 produced. 13C lignin degradation contributed about 3.4% CO2 mineralization during the anaerobic incubation period (1 year). The cumulative lignin-derived C content under aerobic conditions was 11.7% higher than that under anaerobic conditions during four intervals. Lignin-derived microbial biomass C (MBC) accumulation under long-term anaerobic conditions suggests that anaerobic anabolic processes induce an entombing effect, thus promoting SOM accumulation. In the third experiment, SOC, TN, and organic P concentration was significantly related to the diversity of the microbial community and fitted well to linear and quadriatic models, suggesting that SOC, TN, and organic P concentration shaped the microbial community (such as phoD-harboring bacteria). The organic P concentration (such as enzyme-P, a fraction of organic P) shaped the phoD-harboring bacterial diversity and followed the metabolic theory of ecology.Combined, the results show that labile and stable organic matter (OM) are decomposed, transformed, and accumulated by a microbial metabolic pathway in agricultural soil. The low C/N ratios of labile OM (such as root exudates) followed the catabolism with high soil C mineralization. In contrast, the high C/N ratios of root exudates increased microbial biomass with reduced CO2 emission, followed by an anabolic activity for soil C sequestration. The stable OM (i.e., lignin) is also degraded under anaerobic conditions through catabolic activity and partly undergoing stabilization reactions by anabolic activity. The SOC, TN, and organic P concentration affected the microbial communities, particularly in the organic P (i.e., enzyme-P) according to the metabolic theory in response to the microbial process in SOM stabilization.