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To improve soil health and to aid in climate change mitigation, the quantity of soil organic matter (SOM) should be maintained or increased over the long run. In doing so, not only the total quantity of SOC but also the stability of SOC must be considered. Stability of SOC increases as a function of resistance to microbial decomposition or microbial substrate use efficiency through chemical, biological, and physical mechanisms including humification, hydrophobic moieties, molecular diversity, and formation of macroaggregates. One of the mechanisms that enhance stability confers changes in the distribution of C functional groups of SOM. To better understand and quantify how these changes are influenced by agricultural management practices, we collected 670 pairwise data from the body of literature that has evaluated changes in the distribution of C functional groups of SOM measured by solid-state 13C NMR spectroscopy. The types of agricultural managements discussed herein include (1) fertilization, (2) tillage, (3) crop rotation, (4) grazing, and (5) liming practices. Our meta-analyses show that these practices modify the distribution of C functional groups of SOM. Fertilization practices were associated with increased O-alkyl groups. Tillage resulted in increases in the SOC consisted of aromatic and carbonyl groups. Crop rotations, especially legume-based rotations, were found to increase the proportion of aromatic groups. Although there are fewer publications on tillage and crop rotation than on fertilization practices, the distribution of C functional groups may be more influenced by crop rotation and tillage practices than fertilization management—and should be a focus of future research. Supplementary Information The online version contains supplementary material available at 10.1007/s00374-021-01580-2.