Abstract Clay is generally considered an important stabiliser that reduces the rate of decomposition of organic matter (OM) in soils. However, several recent studies have shown trends contradicting this widely held view, emphasising our poor understanding of the mechanisms underlying the clay effects on OM decomposition. Here, an incubation experiment was conducted using artificial soils differing in clay content (0, 5, and 50%) at different temperatures (5, 15, and 25 °C) to determine the effects of clay content, temperature and their interaction on fresh OM decomposition. CO2 efflux was measured throughout the experiment. Phospholipid fatty acids (PLFAs), enzyme activities, microbial biomass carbon (MBC), and dissolved organic carbon (DOC) were also measured at the end of the pre-incubation and incubation periods in order to follow changes in microbial community structure, functioning, and substrate availability. The results showed that higher clay contents promoted OM decomposition probably by increasing substrate availability and by sustaining a greater microbial biomass, albeit with a different community structure and with higher activities of most of the extracellular enzymes assayed. Higher clay content induced increases in the PLFA contents of all bacterial functional groups relative to fungal PLFA content. However, clay content did not change the temperature sensitivity (Q10) of OM decomposition. The higher substrate availability in the high clay artificial soils sustained more soil microbial biomass, resulting in a different community structure and different functioning. The higher microbial biomass, as well as the changed community structure and functions, accelerated OM decomposition. From these observations, an alternative pathway to understanding the effects of clay on OM decomposition is proposed, in which clay may not only accelerate the decomposition of organic materials in soils but also facilitate the SOM accumulation as microbial products in the long term. Our results highlight the importance of clay content as a control over OM decomposition and greater attention is required to elucidate the underlying mechanisms.