Microaggregates play a key role to protect soil organic matter (SOM) from microbial decomposition. Several physical, physico-chemical and biochemical mechanisms have been proposed to describe the SOM stabilization in soil. However, no scientific consensus exists about a range of hypotheses. The aim of this review is to consolidate common notions and hypotheses on physical and physico-chemical protection mechanisms. The key notion of physical protection is exclusion of microbes and enzymes from microaggregate pores. Recent investigations showed higher microbial diversity and presence of accessible pore networks in microaggregates. The physico-chemical protection mechanism is more robust but monolayer or patchy adsorption of SOM onto clay surfaces requires further detailed research. The adsorption of SOM and exo-enzymes on pore walls and clay surfaces has been identified as a plausible concept of SOM stabilization.