<p>Reductive soil disinfestation (RSD) and biochar amendment are effective in suppressing soil-borne pathogens. However, their long-term effects in field applications and impacts on microbial community stability remain poorly understood. In this investigation, we conducted a field experiment with four treatments: CK (without any amendment as the control); BA (biochar amendment); RSD-M (RSD with manure as carbon source); and RSD-MB (RSD with manure as carbon source plus biochar amendment). After 240-day of green pepper cultivation, both RSD-M and RSD-MB treatments maintained lower relative abundance of <i>Fusarium</i>, compared to the CK. After 240 days of green pepper cultivation, the Shannon and Chao1 indices of bacterial and fungal communities in the RSD-M and RSD-MB treatments were significantly lower compared to the CK (<i>P</i> &lt; 0.05). Redundancy analysis identified soil dissolved organic carbon (DOC) and ammonium nitrogen (NH₄⁺-N) contents as the most significant environmental factors influencing microbial communities (<i>P</i> &lt; 0.01). Moreover, microbial co-occurrence network analysis revealed that the RSD-M and RSD-MB treatments exhibited higher network complexity. Cohesion analysis showed that the community stability under the RSD-MB treatment was significantly higher than that of the other treatments. Piecewise structural equation modeling (SEM) analysis indicated that soil DOC and NH₄⁺-N contents influenced fungal diversity, which in turn affected microbial community stability (<i>P</i> &lt; 0.05). The C/N ratio had a direct and significant impact on community stability (<i>P</i> &lt; 0.05). RSD treatments induced distinct responses in bacterial and fungal communities, with bacteria showing higher resilience and fungi being more sensitive after 240-day of green pepper cultivation. Overall, the combination of RSD and biochar enhanced pathogen suppression and promoted greater microbial community stability, providing an effective strategy for soil remediation.</p>