@@@@Highlights •Using 13C NMR to determine the effect of understory fern on SOC chemical composition in pine forests•Understory fern removal decreased microbial abundance and diversity in pine forests.•Understory fern removal decreases SOC recalcitrance via lowering the alkyl C/O-alkyl C ratio.•Understory fern removal altered SOC chemical compositions.•Microbial diversity exerts a greater role than microbial community structure in supporting SOC persistence.