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Introduction Faecal calprotectin (FC) is the standard noninvasive biomarker for monitoring inflammatory bowel disease (IBD) but has substantial logistical barriers, high processing costs, and a sizeable environmental footprint. As the NHS commits to Net Zero emissions by 2040, identifying lowercarbon alternatives is increasingly important. Quantitative faecal immunochemical testing (qFIT) is automated, postalfriendly, and scalable for highvolume IBD pathways. We compared qFIT with FC for monitoring colonic IBD, incorporating patient acceptability and carbonfootprint analyses.Methods This is a prospective longitudinal diagnostic-accuracy sub-study within the multicentre MUSIC cohort. Adults with active ulcerative colitis (UC) or colonic/ileocolonic Crohn’s disease (CD) provided paired qFIT and FC at up to five visits over 12 months. The primary outcome was endoscopic mucosal healing at ~6 months (MES 0 for UC; SES-CD for CD). Optimal thresholds were derived using Youden’s index and AUCs compared using DeLong tests. Patient acceptability was assessed via a UK-wide patient survey comparing FC and qFIT. Carbon footprint per test was estimated using a simplified life-cycle assessment (kg CO2e/test) from kit manufacture to disposal.Results 136 participants (73 UC, 63 CD) contributed 439 paired qFIT/FC samples. Both biomarkers were higher during clinically active disease than remission (p<0.001). For clinical activity, qFIT and FC performed similarly (AUC 0.68 vs 0.71, p=0.39), while a combined qFIT+FC model improved discrimination (AUC 0.83). Among 104 participants with baseline and ~6-month endoscopy, 48 (46.2%) achieved mucosal healing. qFIT and FC predicted mucosal healing equivalently (AUC 0.72 vs 0.72; p=1.0), with optimal thresholds of 7 ug Hb/g and 71 ug/g, respectively. At standard cut-offs (qFIT 10 ug haemoglobin/g; FC 250 ug/g), 318/439 (72.4%) pairs were concordant. Discordance was mainly qFIT-high/FC-low (84/439, 19.1%) versus qFIT-low/FC-high (37/439, 8.4%). Among 121 patients who had experienced both tests, qFIT was consistently rated higher for ease of sampling, processing, return and overall acceptability (all p<0.001), with 40.5% preferring qFIT for ongoing monitoring (vs 14.0% for FC). Carbon emissions per test were ~14-fold lower with qFIT than FC (0.075 vs 1.05 kg CO2e per test).Conclusions In colonic IBD, qFIT performs equivalently to FC for monitoring disease activity and predicting mucosal healing, while being more acceptable to patients and generating substantially lower carbon emissions. A qFITfirst monitoring pathway aligns with NHS Net Zero priorities, reduces environmental and operational burden, and may allow FC to be reserved for discordant results or assessment of smallbowel CD.