The demand of renewable energy has increased the interest in whole-tree harvesting. The sustainability of whole-tree harvesting after clear-cutting, from an acidification point of view, depends on two factors: the present acidification status and the further loss of buffering capacity at harvesting. The aims of this study were to investigate the relationship between these two factors at 26 sites along an acidification gradient in Sweden, to divide the sites into risk classes, and to examine the geographical distribution of them in order to provide policy-relevant insights. The present status was represented by the acid neutralizing capacity (ANC) in soil solution, and the loss of buffering capacity was represented by the estimated exceedance of critical biomass harvesting (CBH). The sites were divided into three risk classes combining ANC and exceedance of CBH. ANC and exceedance of CBH were negatively correlated, and most sites had either ANC < 0 and exceedance (high risk) or ANC > 0 and no exceedance (low risk). There was a geographical pattern, with the high risk class concentrated to southern Sweden, which was mainly explained by higher historical sulfur deposition and site productivity in the south. The risk classes can be used in the formulation of policies on whole-tree harvesting and wood ash recycling.