Background: Perforation peritonitis is amongst the most common surgical emergencies in India, differing in etiology and outcomes from Western populations. The contaminating microorganisms are usually polymicrobial, and even fungal isolates are increasingly reported. This study aimed to evaluate the microbiological profile and fungal culture positivity in perforation peritonitis. Methods: This was a prospective randomized, controlled crossover study which was conducted in the Department of General Surgery, Government Medical College & Rajindra Hospital, Patiala on 70 patients admitted with acute abdomen and were diagnosed with perforation peritonitis. Exploratory laparotomy was performed, and intraoperative peritoneal fluid was examined for bacterial and fungal cultures. Results: In this study, the mean age of patients was 38 years with a male predominance (~75%), similar to Indian series but younger than Western reports. Ileal (44%) and gastroduodenal (39%) perforations were the most common, in contrast to western data where peptic ulcer perforations predominate. Surgical management included Graham’s omental patch repair (54%), primary repair (40%), and ileostomy (20%), aligning with accepted practices. Bacterial cultures were positive in 56% of cases, with E. coli (44%) being the most frequent isolate, followed by gram-positive cocci (24%) and Klebsiella (18%). Fungal culture positivity was observed in 56% cases, most commonly Candida albicans (37%), which correlated with prolonged ICU stay, higher surgical site infection, and increased mortality. Overall mortality was 11.4%, primarily due to delayed presentation and sepsis. Conclusion: As per our study, perforation peritonitis was most commonly diagnosed in younger males and was most often due to ileal perforations. Routine bacterial and fungal culture of peritoneal fluid are essential to guide the therapy. Early surgical intervention, targeted antimicrobial treatment, and consideration of empirical antifungal therapy in high-risk cases are critical to improving outcomes.