Manganese (Mn) is a critical element in soils, essential to plant growth. Long-term and intensively managed Lei bamboo (Phyllostachys violascens) stands are usually subjected to severe soil acidification and Mn activation. However, Mn migration from topsoil to deep soil induced by severe soil acidification was poorly recognized and studied. The distribution and changes of the total and the operationally defined Mn forms in soil profiles and its potential stress and environmental effect were investigated in a chronosequence of Lei bamboo stands (0, 2, 6, 11, and 16 years of stand age). The results showed that the Mn amount was significantly decreased in topsoil and accumulated in subsoil with the long-term and intensive fertilizer application. Soil exchangeable Mn and superphosphate extractable Mn demonstrated large different variation to total Mn, whereas their sum was largely higher than and highly correlated with 8-hydroxyquinoline (HQN) extractable Mn. Soil organic carbon, pH value, exchangeable bases, and soil redox simultaneously controlled soil Mn depletion. In conclusion, long-term and intensive fertilizer application leads to soil acidification and accelerated soil Mn depletion in bamboo stand soil, promoting Mn accumulation in bamboo shoots.