Background Globally, infectious diarrhea poses a serious threat to public health, especially in emergency department (ED) settings where timely and efficient treatment is essential. The primary objective of this study was to explore and evaluate the efficacy of a multidisciplinary approach (MDA) in the management of infectious diarrhea within the ED setting. Methodology This prospective cohort study was conducted from January to December 2023 at the Lady Reading Hospital ED in Peshawar, Pakistan. Individuals 18 years of age or older with a confirmed diagnosis of infectious diarrhea were included in the study. Those who refused to participate or had non-infectious reasons were excluded from the study. Through successive sampling, 650 patients comprised the study sample. Using a standardized form, demographic information, clinical presentations, test results, treatment methods, and patient outcomes were collected. Descriptive statistics and logistic regression were used in statistical studies to assess treatment outcomes and complications. Results Of the 650 patients, the majority (203 patients, 31.23%) were between the ages of 30 and 39 years. The gender distribution was about equal (332 men, 51.08%; 318 females, 48.92%). Abdominal pain (383 patients, 58.92%) was the most common presenting complaint. In 310 instances, bacterial pathogens were found, 160 had viral infections, and 110 had parasitic infections. There were notable complications, such as sepsis (37 patients, 5.69%), although the response to treatment effectiveness was notably high (593 patients, 91.08%). Upon follow-up, 590 (90.77%) patients had symptom and sign resolution, while 80 (12.31%) patients had a low recurrence rate. Longer symptom duration (odds ratio (OR) = 1.45, 95% confidence interval (CI) 1.12-1.88, p = 0.005) and specific antibiotics (OR = 1.68, 95% CI = 1.25-2.25, p = 0.001) were found to improve treatment success using logistic regression, whereas the risks of complications increased with age (OR = 1.05, 95% CI = 1.01-1.09, p = 0.012) and severe dehydration (OR = 1.75, 95% CI = 1.32-2.31, p < 0.001). Conclusions The MDA to manage infectious diarrhea in the ED significantly improved patient outcomes and reduced complications.