Natural regeneration practices are significant for cost-effective management, but they are associated with difficulty in controlling species composition. Among various factors, soil properties (such as water content and nutrient) would be significant because they are drastically changed by the practice especially when heavy machinery is applied. We therefore evaluate influences of different machinery practices on vegetation development during the initial 3-years, with emphasis on changing soil properties. There were no significant relationships of soil properties with the number of seedlings germinated. However, at the later stage (3rd year), practices with leaving surface soil resulted in more herbaceous dominant vegetation. The possible mechanisms to produce the pattern, including difference in responses between herbaceous and tree species, are discussed.