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Recent advances in the integration of artificial intelligence (AI) and microbiome analysis have expanded our understanding of gastrointestinal diseases, particularly in inflammatory bowel disease (IBD), colitis-associated colorectal cancer (CAC), and sporadic colorectal cancer (CRC). While IBD and CAC are mechanistically linked, recent evidence also implicates dysbiosis in sporadic CRC. The progression from IBD to CAC is mechanistically linked through chronic inflammation and microbial dysbiosis, whereas distinct dysbiotic patterns are also observed in sporadic CRC. In this review, we examine how machine learning (ML) and AI are applied to the microbiome and multi‑omics data which enables the discovery of non‑invasive microbial biomarkers, refined risk stratification, and prediction of treatment response. We highlight how emerging computational frameworks, including explainable AI (xAI), graph‑based models, and integrative multi‑omics, are advancing the field from descriptive profiling toward predictive and prescriptive analytics. While emphasizing these innovations, we also critically assess current limitations, including data variability, lack of methodological standardization, and challenges in clinical translation. Collectively, these developments enable AI‑powered microbiome research as a driving force for precision medicine in IBD, CAC, and sporadic CRC.