Background: Colorectal cancer (CRC) ranks third in incidence and fourth in cancer-related mortality worldwide. It typically begins as benign polyps that may progress to malignancy through cumulative genetic alterations. Inflammatory bowel disease (IBD) is a major risk factor for CRC, and Mycobacterium avium subspecies paratuberculosis (MAP) has been implicated in its pathogenesis and may also contribute to CRC development, particularly in regions with MAP-infected livestock. Methods: In this case-control study which included 147 participants, we analyzed 74 patients with colorectal conditions, encompassing both precancerous and cancerous types, alongside 73 healthy controls (HCs). The Participants underwent colonoscopy at a clinical center in Golestan province, and provided informed consent and relevant health data. Exclusion criteria included recent antibiotic use and a history of gastrointestinal disease. Genomic DNA was extracted from intestinal mucus samples and analyzed using nested PCR. Results: In our study, the prevalence of MAP was significantly higher in precancerous (46.7%) and cancerous patients (57.1%) compared to HCs (13.3%, p < 0.0001), suggesting a possible association with disease progression that warrants further investigation. Conclusion: The study highlights a strong association between MAP and colorectal neoplasia, especially in patients with precancerous and cancerous conditions. Despite no notable differences in lifestyle factors between groups, MAP’s prevalence points to its potential influence on CRC progression. This warrants further investigation into MAP’s role in CRC, particularly in regions with MAP-infected livestock, for public health insights and prevention strategies.