Intensive harvesting of forest biomass for bioenergy has the potential to degrade forest soils and productivity if ecosystem carbon and other nutrients are depleted faster than replenished naturally or by management inputs. Climate change mitigation potential associated with bioenergy may be threatened if forest management operations reduce soil carbon stocks. Research reported here was initiated in 1979 to determine the effects of whole-tree harvesting on long-term site productivity and ecosystem carbon and nutrient pools and fluxes in a northeastern North American temperate balsam fir-red spruce forest. A sequence of harvesting and silvicultural treatments were applied from 1981 to 1993 using a paired-watershed experimental design. Treatments included whole-tree clearcutting, stem-only harvesting, simulated by return of chipped or lopped delimbing residue, conifer release by applying herbicide, and pre-commercial thinning and fertilizer application. Quantitative samples of the forest floor were excavated in 2016. Quantitative soil pits were sampled in 2017 to a depth of 50 cm below the forest floor, where possible; the basal till subsoil was sampled to a depth of 100 cm with an auger. Forest floor samples were analyzed for total carbon, nitrogen, phosphorus, potassium, calcium, magnesium and aluminum. Organic and mineral soil layer samples from the quantitative pits were analyzed for pH, short and long-lived soil carbon via ¹³C cross polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR), total carbon and nitrogen and extractable phosphorus, potassium, calcium, magnesium and aluminum. Forest floor carbon and nitrogen on whole-tree harvested plots 35 years after harvest were about 50% of the amount on the unharvested watershed. Stem-only harvesting partially mitigated the reduction, and gross losses were apparently offset by increases in the mineral soil solum to depth 50 cm, suggesting that downward translocation of soil organic matter was a significant ecosystem process during the 35 years since harvest. Accumulated forest floor and mineral soil stock of total carbon and nitrogen and extractable nutrients to depth 100 cm did not differ significantly between the harvested and unharvested watershed. A corresponding similarity in mineral soil pools of extractable phosphorus and non-acid cations in the two watersheds suggests that inputs from atmospheric deposition, primary and secondary mineral weathering, organic matter mineralization and litterfall balanced exports including leaching and plant uptake. Ecosystem stocks of extractable phosphorus, base cations, and total organic carbon and nitrogen were maintained 35 years after whole-tree harvesting of a primary spruce-fir forest.