Compost prepared using pruning material (PM) contains a higher amount of mineralizable carbon (C) than conventional compost, readily causing nitrogen (N) immobilization in soil due to the multiplication of microorganisms and subsequently likely causing N starvation for plant growth inhibition. However, organic matter mineralization in soil is affected by soil microbial activity, which correlates with the total C and N contents. Therefore, we hypothesized that application of PM compost to different fertility soils have different effects on plant growth depending on soil microbial activity. Using an incubation experiment, we found that the application of PM compost had a priming effect in forest soil and subsoil, causing N immobilization in both soils. However, the period of N immobilization depended on soil microbial activity, being shorter when the soil microbial activity was higher. To test the effects of PM compost on plant growth, we grew komatsuna (Brassica rapa L. var. perviridis LH Bailey) in different soils with equal applications of PM compost for 1 month. We found that PM compost application significantly inhibited plant growth in the subsoil (P < 0.05), but significantly accelerated plant growth in the forest soil (P < 0.05), suggesting that different effects are observed on plant growth in soils with different microbial activities. In conclusion, these findings indicate that the application of PM compost to soil can accelerate plant growth in soils with high microbial activities, but can inhibit plant growth in soils with low microbial activities.