We aimed to reveal how soil environment and microbial communities influence decomposition in cool-temperate deciduous forests underlain by serpentine rock and limestone. The present study was conducted in (1) the serpentine and non-serpentine (mudstone) sites on Mt. Oe, Kyoto, and (2) the karst and non-karst (sandstone) sites on Mt. Ibuki, Shiga in Japan. We had a priori hypothesis that decomposition is faster in the non-serpentine and karst sites owing to their higher soil moisture availability. In summer 2020, we performed a decomposition experiment by placing three types of substrates different in nutrients and cellwall components. On Mt. Oe, the non-serpentine site showed higher decomposition rate of nutrient-rich green tea than the serpentine site. On Mt. Ibuki, the karst site exhibited lower decomposition rate of the green tea than the non-karst site. On both mountains, decomposition rate of cellulose and coffee filters that are mostly compose of cellwall components did not differ between the sites. In the serpentine site, we found higher fungal abundance in the decomposed substrates, indicating that it offset the negative influence of soil moisture content in decomposition of cellulose and coffee filters. The lower or similar decomposition rate in the karst site remains as an open question.