Introduction Acute fascia dehiscence (FD) is a threatening complication occurring in 0.4–3.5% of cases after abdominal surgery. Prolonged hospital stay, increased mortality and increased rate of incisional hernias could be following consequences. Several risk factors are controversially discussed. Even though surgical infection is a known, indisputable risk factor, it is still not proven if a special spectrum of pathogens is responsible. In this study, we investigated if a specific spectrum of microbial pathogens is associated with FD. Methods We performed a retrospective matched pair analysis of 53 consecutive patients with an FD after abdominal surgery in 2010–2016. Matching criteria were gender, age, primary procedure and surgeon. The primary endpoint was the frequency of pathogens detected intraoperatively, the secondary endpoint was the occurrence of risk factors in patients with (FD) and without (nFD) FD. Results Intraabdominal pathogens were detected more often in the FD group (p = 0.039), with a higher number of Gram-positive pathogens. Enterococci were the most common pathogen (p = 0.002), not covered in 73% (FD group) compared to 22% (nFD group) by the given antibiotic therapy. Multivariable analysis showed detection of Gram-positive pathogens, detection of enterococci in primary laparotomy beside chronic lung disease, surgical site infections and continuous steroid therapy as independent risk factors. Conclusion Risk factors are factors that reduce wound healing or increase intra-abdominal pressure. Furthermore detection of Gram-positive pathogens especially enterococci was detected as an independent risk factor and its empirical coverage could be advantageous for high-risk patients.