Drainage-induced changes in wetland soil organic carbon (SOC) composition and origin are poorly investigated compared to SOC stocks. Here, using soil fractionation and neutral sugars, we find that long-term drainage increased both plant- and microbial-dominated (i.e., light and mineral-associated, respectively) fractions in a fen while microbial residues increased at the expense of plant residues in a drained bog, accompanied by divergent changes of SOC contents. These findings highlight stimulated soil “microbial carbon pump” in drained wetlands, whose efficiency deserves further investigation related to wetland SOC persistence.