Introduction Amoebiasis, caused by the protozoan parasite , remains a significant public health concern in our country due to its endemicity. It poses a unique challenge in patients with inflammatory bowel disease (IBD), where its symptoms often mimic disease flare-ups, leading to diagnostic uncertainty and potential delays in appropriate management. The overlap in clinical presentation between amoebiasis and IBD exacerbations can result in misdiagnosis or inappropriate treatment, further complicating patient outcomes. In this context, our study was designed to explore and describe the epidemiological profile of intestinal amoebiasis specifically in the IBD patient population. By identifying patterns of co-infection, risk factors, and clinical manifestations, we aim to enhance early recognition and guide targeted diagnostic and therapeutic strategies. This is particularly important for improving outcomes and optimizing care in regions where amoebiasis remains endemic. Materials and methods This retrospective study examined 684 stool samples from IBD patients sent to the central parasitology-mycology laboratory at Ibn Sina University Hospital in Rabat between June 2014 and July 2022. A positive diagnosis was established through parasitological examination of stool (PES) samples using a combination of fresh examination and two concentration techniques: Merthiolate-Iodine-Formol and Bailenger. Results Of the 684 stool samples collected from patients with IBD, 162 tested positive, representing a prevalence rate of 24%. Of these, 78 were from patients with ulcerative colitis (UC), 67 with Crohn's disease (CD), and 17 with indeterminate IBD. Twenty patients were in remission at the time of the study: ten with UC, seven with CD, and three with unspecified IBD. The majority of patients were adults (159 cases), with a female predominance (sex ratio M:F = 0.7). In our study, intestinal parasitism showed a predominance of (60%), followed by the cystic form of the parasite (23%). Both forms were present in 14% of cases. Conclusion According to the literature, amoebiasis can mimic or exacerbate the clinical manifestations of IBD, complicating the differential diagnosis and increasing the risk of inadequate treatment in the absence of systematic PES samples. These results corroborate the findings of our study, which highlight the need for early diagnosis and appropriate management of IBD to prevent complications.