This study aims to evaluate HM (high methoxyl) pectin from different sources (apple, citrus, and beet) with varying degrees of methyl esterification (DOE) to identify the optimal grade for colonic bacterial enzyme-triggered polymeric coatings for colon-targeted delivery of drugs. Drug-loaded multiparticulates were prepared by a powder layering technique and subsequently coated into distinct trial formulation batches with ethyl cellulose and different HM pectin-based plasticized coating solutions. Otilonium bromide, a model drug for irritable bowel syndrome, was employed. Drug-polymer compatibility was confirmed through FT-IR and DSC studies. The coated multiparticulates demonstrated high drug entrapment efficiency (>85%), favorable micromeritic properties, and minimal loose surface drug crystals (<1.2%). Among the batches, F48 (p = 0.0042), coated with apple pectin (DOE 50%), exhibited superior colon-targeting efficiency, limiting drug release to 15.47 ± 1.53% under simulated upper gastrointestinal conditions while achieving 78.27 ± 2.11% release under colonic conditions by the ninth hour in vitro. Surface topography was analyzed via scanning electron microscopy before and after dissolution. In vivo, X-ray roentgenography, and gamma-scintigraphy studies in New Zealand white rabbits further validated the colon-targeting efficacy of the optimized batch. The source and DOE value of the HM pectin were found to affect premature drug release and colon-targeting efficiency. Apple HM pectin 50% DOE was found to be the ideal HM pectin for microbial enzyme-dependent colon-targeted coatings.