Alterations in forest productivity and changes in the relative proportion of above- and belowground biomass may have nonlinear effects on soil organic matter (SOM) storage. To study the influence of plant litter inputs on SOM accumulation, the Detritus Input Removal and Transfer (DIRT) Experiment continuously alters above- and belowground plant inputs to soil by a combination of trenching, screening, and litter addition. Here, we used biogeochemical indicators [i.e., cupric oxide extractable lignin-derived phenols and suberin/cutin-derived substituted fatty acids (SFA)] to identify the dominant sources of plant biopolymers in SOM and various measures [i.e., soil density fractionation, laboratory incubation, and radiocarbon-based mean residence time (MRT)] to assess the stability of SOM in two contrasting forests within the DIRT Experiment: an aggrading deciduous forest and an old-growth coniferous forest. In the deciduous forest, removal of both above- and belowground inputs increased the total amount of SFA over threefold compared with the control, and shifted the SFA signature towards a root-dominated source. Concurrently, light fraction MRT increased by 101 years and C mineralization during incubation decreased compared with the control. Together, these data suggest that root-derived aliphatic compounds are a source of SOM with greater relative stability than leaf inputs at this site. In the coniferous forest, roots were an important source of soil lignin-derived phenols but needle-derived, rather than root-derived, aliphatic compounds were preferentially preserved in soil. Fresh wood additions elevated the amount of soil C recovered as light fraction material but also elevated mineralization during incubation compared with other DIRT treatments, suggesting that not all of the added soil C is directly stabilized. Aboveground needle litter additions, which are more N-rich than wood debris, resulted in accelerated mineralization of previously stored soil carbon. In summary, our work demonstrates that the dominant plant sources of SOM differed substantially between forest types. Furthermore, inputs to and losses from soil C pools likely will not be altered uniformly by changes in litter input rates.