Abstract Background Diarrhea is a serious complication noted in colorectal cancer (CRC) patients undergoing cytotoxic chemotherapy, which impacts both their quality of life and treatment adherence. Here, we assessed the safety and efficacy of fecal microbiota transplantation (FMT) for chemotherapy-induced diarrhea (CID) management in patients with CRC. Methods This open-label, single-arm trial included 20 CRC patients experiencing grade 2 or 3 CID, in whom conventional standard antidiarrheal treatments had been ineffective. A single course of FMT was administered within a 2-week interval. Each course consisted of 90 capsules (totaling approximately 18 × 10¹¹ CFU bacteria), administered orally three times a day on days 1, 2, and 3. The patients’ changes in diarrhea severity, microbiome composition (16S rRNA gene sequencing), and immune function (flow cytometry) were assessed before and after FMT (over 12 weeks). Results Diarrhea cessation was noted in 17 (85%) of all 20 patients after one or more FMT cycles over at least 12 weeks. FMT also led to significant improvements in gut microbiota diversity along with significant increases in B (CD19⁺) cells (p = 0.0001), cytotoxic T ( CD3⁺CD8⁺) cells (p = 0.0010), and natural killer cells (p = 0.0002). No major adverse events were noted. Conclusions Our preliminary evidence suggests that FMT is a safe, potentially effective approach for managing CID in patients with CRC. Trial registration: Chictr.org.cn, ChiCTR2100049431 (Date assigned: Agusta 8, 2021). https://www.chictr.org.cn/showproj.html?proj=131083
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