Abstract Background: Modulation of gut dysbiosis with Fecal Microbiota Transplantation (FMT) is a novel modality and has shown promising results in decompensated cirrhosis (DC). We explored the impact of FMT on prognostic scores, complications, ammonia levels, inflammatory markers [(Interleukin -1 (IL-1) and 6 (IL-6)], and 180-day mortality in DC. Methods: Consecutive patients with DC (MELD12-21) were assigned to either FMT (FMT group) delivered as 30gm freshly prepared stool (from a related stool donor) homogenized in 100 ml of normal saline through a nasojejunal tube or standard of care therapy (SOC group). Outcomes were assessed on days 7, 28, 90, and 180. Results: Eighteen patients each with comparable baseline characteristics (88.8% males; mean age, 46.12±6.23 vs. 47.0±4.54; mean CTP, 9.5±0.71 vs. 9.6±0.80; mean MELD, 16.1±1.71 vs. 1.62±1.81) were allocated to FMT or SOC . Although significant differences were noted in the CTP score on day 7 (P=0.02) and day 90 (P=0.01), MELD and MELD-Na scores were similar at all time points. A non-significant reduction in ammonia levels was seen on day 7 and day 28 (P=0.21 and P=0.17; respectively). IL-1 (P=0.01) and IL 6 (P=0.005) levels reduced significantly on day 28. New-onset variceal bleed (P=0.70), breakthrough hepatic encephalopathy events (P=0.61) and 180-day survival (HR, 2.02; 95% CI, 0.37-11.05; P=0.41). were similar. Although transient gastrointestinal side-effects were common (56.2%), no serious adverse events were noted. Conclusion: Single session FMT in DC is safe and leads to selective improvement of CTP scores and systemic inflammatory markers but offers no survival benefit. (ClinicalTrials.gov number, NCT04842539)