Soil organic matter (OM) represents a key C pool for climate regulation but also an essential component for soil functions and services. Scientific research in the 21st century has considerably improved our knowledge of soil organic matter and its dynamics, particularly under the pressure of the global disruption of the carbon cycle. This paper reviews the processes that control C dynamics in soil, the representation of these processes over time, and their dependence on variations in major biotic and abiotic factors. The most recent advanced knowledge gained on soil organic matter includes the following. (1) Most organic matter is composed of small molecules, derived from living organisms, without transformation via additional abiotic organic polymerization; (2) microbial compounds are predominant in the long term; (3) primary belowground production contributes more to organic matter than aboveground inputs; (4) the contribution of less biodegradable compounds to soil organic matter is low in the long term; (5) two major factors determine the soil organic carbon production “yield” from the initial substrates: the yield of carbon used by microorganisms and the association with minerals, particularly poorly crystalline minerals, which stabilize microbial compounds; (6) interactions between plants and microorganisms also regulate the carbon turnover time and therefore carbon stocks; (7) among abiotic and biotic factors that regulate the carbon turnover time, only a few are considered in current modeling approaches (i.e., temperature, soil water content, pH, particle size, and sometimes C and N interactions); and (8) although most models of soil C dynamics assume that the processes involved are linear, there are now many indications of nonlinear soil C dynamics processes linked to soil OM dynamics (e.g., priming). Farming practices, therefore, affect soil C stocks not only through carbon inputs but also via their effect on microbial and organomineral interactions, yet it has still not been possible to properly identify the main mechanisms involved in C loss (or gain). Greater insight into these mechanisms and their interdependencies, hierarchy and sensitivity to agricultural practices could provide future levers of action for C sequestration in soil.