Global environmental change is altering the quality and quantity of plant inputs into soil. However, it is unclear how these long-term changes may fundamentally shift the biogeochemistry of soil carbon in forests. To better understand how varied detrital inputs alter soil organic matter (OM) biogeochemistry and composition at the molecular-level, soil samples were collected from a 20 year detrital manipulation experiment in an old-growth coniferous rainforest in Western Oregon. The experiment includes ambient (control) plots and six treatments: Double Litter, Double Wood, No Roots, No Litter, No Inputs and OA-less (replacement of O and A horizons with B horizon). Total soil carbon and nitrogen, molecular-level OM composition using solid-state 13C nuclear magnetic resonance, and targeted compound extractions were measured. Although soil carbon did not increase with Double Litter and Double Wood, microbial biomass and the decomposition of specific forms of soil OM (i.e., cellulose) increased, likely due to sustained soil priming over 20 years. Mineral (0–10 cm) soil carbon was similar across litter exclusion treatments (No Litter, No Roots, No Inputs), however, soil OM decomposition increased relative to the control. Microbial-derived lipids increased under Double Litter but decreased when above-ground litter was excluded. Notably, needle-derived lipids decreased with above-ground litter exclusion and root-derived compounds did not change under below-ground root exclusion. These results suggested that above-ground litter alters soil carbon biogeochemistry in surface soils to a greater extent than below-ground inputs. This study also demonstrated that long-term soil carbon biogeochemical trajectories were mostly governed by litter quality, quality and microbial processing of above-ground inputs.