The effects of three postharvest organic matter removal treatments on fermentation-humus (FH) layer and soil characteristics were compared in replicated trials in four second rotation New Zealand Pinus radiata plantation forests, planted 8–16 years prior to sampling. All sites were sampled in early 2002 and 2003. Increasing organic matter removal significantly decreased the mass of the FH layer in the treatment plots, the moisture content in the FH layer and mineral soil, the concentration of carbon in the FH layer and mineral soil, the pool of carbon stored in the FH layer, the concentration of nitrogen in the mineral soil and the pool of nitrogen stored in the FH layer. Mineral soil pH was significantly increased with increasing organic matter removal. The persistence of the significant differences in the FH layer and mineral soil characteristics strongly suggested that variations in organic matter removal have long-term effects on forest floor properties, and significantly influences carbon storage over the life of the rotation.