Introduction: Inflammatory bowel disease (IBD) is a complex condition with an unknown etiology, although dysbiosis of the gut microbiota has been proposed as a potential contributing factor. Despite this, the specific changes in gut microbiota in IBD patients, particularly during active flare-ups and remission , compared to healthy individuals, are not yet well understood. The goal of this study was to explore the microbial alterations occurring in the gut during both the exacerbation and remission phases of IBD and to contrast these changes with those in healthy control subjects. Patients and Methods: The current study involved eleven patients with inflammatory bowel disease (IBD) and nine healthy control subjects. Nine IBD patients were available for follow-up, enabling repeat sample collection after confirming their disease status. This was an observational-analytical study, aimed to examine changes in the gut microbiota of IBD patients without any interventions. Observation & Results: Our findings show that the total bacterial count was significantly higher in the non-IBD control group compared to both the exacerbated IBD group and the follow-up group. In exacerbated IBD patients, bacterial counts were lower than during remission, with qPCR analysis revealing a sharp decline in bacterial count during flare-ups, followed by an increase as patients transitioned into remission. Conclusion: Despite the ongoing uncertainty about the link between gut microflora and inflammatory bowel disease (IBD), our study and previous reports suggest that dysbiosis in gut microbiota, may contribute to acute IBD exacerbations. A reduction in microbiota , capable of producing short-chain fatty acids (SCFAs) could promote intestinal inflammation, while an increase in harmful bacterial communities may worsen the disease. Future research on restoring beneficial bacteria with prebiotics and probiotics may offer insights into improving IBD prognosis.