The practice of harvesting forest residues is rapidly increasing due to rising demand for renewable energy. However, major concerns have been raised about the sustainability of this practice and its net impact on long term soil ability to support forest productivity, particularly through second and subsequent rotations. In this study, soil chemical properties such as acidity, total N and C, available NO3–N and NH4–N and exchangeable cations were measured in all horizons in peaty gleys soils under one of the oldest experiments in Europe—a 28-year-old second rotation stand of Sitka spruce (Picea sitchensis), in Kielder forest, UK. Treatments included Whole Tree Harvesting (WTH—of all above ground biomass), Conventional stem-only harvesting (CH) of the first rotation crop, and repeated Fertilisation (FE) after the planting of the second rotation forest. This study demonstrates the soil changes underpinning the reduced second rotation tree productivity on these acidic upland sites under WTH, a further 18 years after the investigation by Proe and Dutch (1994). Overall, WTH increased soil acidity significantly (p < 0.05) and reduced soil base saturation whilst FE reduced soil acidity (p < 0.05) and increased soil base saturation as compared to CH. Soil moisture was significantly higher (p < 0.01) under WTH compared to CH and FE plots. There was no evidence that WTH decreased soil organic carbon (SOC) and soil nitrogen (N), but to the contrary there were significantly (p < 0.01) higher concentrations and stocks of total C and N in the WTH soils compared with CH and FE. The depletion of SOC and N in CH and FE plots was attributed to much higher soil mineralisation rates associated with the brash and fertilisation as compared to the WTH plots, where significantly less soil available NO3–N (p < 0.01) was found. In the long term WTH on peaty gley soils appears positive for soil C and N storage. However, WTH had a long term negative impact on soil and tree nutrition of K+ and P, which are currently at deficient levels, but has had a stabilising effect on tree N nutrition as measured in twigs and needles. These results suggest that whilst WTH lead to a reduction in aboveground tree biomass compared to conventional harvest, these practices on selected soil types and certain sites may be beneficial for soil C and N sequestration. The overall findings of this study imply that cost benefit analyses for each site should be carried out before decisions are made on the appropriate type of forest operations (harvesting and replanting), considering both geology and soils in order to serve both environmental benefits, long term sustainability and the available biomass production for timber and biofuel.