Oil palm plantations generate substantial biomass waste, primarily old oil palm trunks (OPT), during replanting. As part of a sustainable plantation management program, old OPT are returned to the plantation and released nutrients into the soil for new oil palm seedlings. However, whether this method improves soil nutrient levels is unclear. In this study, we investigated the effects of OPT on oil palm seedling growth and soil microbial communities. The plant height, chlorophyll content, leaf area, and biomass weight were low in seedlings grown in soil containing OPT [44.3 cm, 44, 278.9 cm2, 19.6 g (dry shoot), and 14.9 g (dry root)]. Similar results were obtained for seedlings grown in soil containing cellulose or soil containing OPT and fertiliser. Leaf nitrogen, phosphorus, and potassium contents were similar in seedlings grown in soil amended with OPT and control seedlings. However, the calcium content was significantly lower in seedlings grown in soil containing OPT (0.424 ± 0.004%) than in control seedlings (0.496 ± 0.006%). Metagenomic analysis of soils showed that three lignocellulose-degrading fungal genera (Chaetomium, Mortierella, and Staphylotrichum) were abundant in soil containing OPT. Thus, the return of OPT promotes the growth of lignocellulose-degrading microorganisms and decreases fertiliser nutrient availability.