Reforestation with native species and resulting understory succession can exert important influences on soil organic matter (SOM) storage and chemistry, but a mechanistic understanding of these effects is lacking. We studied different aged Masson pine (Pinus massoniana L.) plantations with and without the understory fern, Dicranopteris dichotoma (Thunb.) Berhn., in subtropical China to assess how SOM over a 30 year sequence of pine growth and fern expansion. To do this, we measured total SOM, lignin-derived phenols, soil carbon (total C and 13C), soil nitrogen (total N and 15N), and soil microbial community composition via phospholipid fatty acid (PLFA) analyses. We found that the accumulation of newly-formed SOM outweighed decomposition of old SOM, with the majority of this increase being derived from fern detrital inputs. Where ferns were present, ferns contributed 54–61% of total soil C storage in surface (0–10 cm depth) soils, which was 62–91% higher than pre-reforestation soil C storage. We found that the abundance of lignin-derived compounds was lower in fern dominated soils, perhaps because soils under ferns supported more soil fungi, the primary decomposers of the lignin in soil. Fern soils also showed higher ratios of syringyls to vanillyls and decreased δ13C values, an indicator that ferns altered the composition of SOM at the molecular level while contributing significantly to SOM accumulation. Reforestation especially when accompanied by fern expansion also improved soil N and phosphorus (P) status, with observed declines in soil δ15N in fern dominated soils aligning with increased nutrient retention and observed increases in soil C storage. Our study highlights the potentially important role of understory ferns in mediating SOM chemistry and soil C storage during ecosystem recovery.