Soil organic matter (SOM) is a crucial component of soil, through which physical, chemical, and biological characteristics interact in a local context. Within the forest category, the conversion of natural forests to monoculture plantations has raised concerns in Indonesia over the loss of soil functions, similar to conversion to agriculture. In natural forests, SOM can accumulate as part of a closed nutrient cycle with minimal nutrient losses; in plantation forestry, SOM decline and recovery can alternate over time, associated with larger nutrient losses. We reviewed existing studies to quantify how shifts from natural forests to short-rotation plantation forests (SRPF) affect SOM dynamics, soil nutrient contents, and soil-borne pathogens that cause disease. The review combines descriptive and quantitative methods (meta-analysis). The results show that conversion affects the soil C balance, soil structure and water balance, soil nutrient balance, and soil-borne diseases. Contributing factors include the reduced diversity of plant and rhizosphere communities, lower annual litter production, more uniform litter quality, and nutrient removal at the harvest cycle. Conversion from natural to plantation forest conditions also increases plant disease incidence by changing biological control mechanisms.