Certifications are an increasingly used tool of quality management in the health care system. The primary goal is to improve the quality of treatment due to implemented measures based on a defined catalog of criteria and standardization of the treatment processes. However, the extent to which this affects medical and health-economic indicators is unknown. Therefore, the study aims to examine the possible effects of the certification as a Reference Center for Hernia Surgery on the treatment quality and reimbursement dimensions. The observation and recording periods were defined as 3 years before (2013–2015) and 3 years after certification as a "Reference Center for Hernia Surgery" (2016–2018). Possible changes due to the certification were examined based on multidimensional data collection and analysis. In addition, the aspects of structure, process and result quality, and the reimbursement situation were reported. One thousand three hundred and nineteen cases before and one thousand four hundred and three cases after certification were included. After the certification, the patients were older (58.1 ± 16.1 vs. 64.0 ± 16.1 years, p < 0.01), had a higher CMI (1.01 vs. 1.06), and a higher ASA score (< III 86.9 vs. 85.5%, p < 0.01). The interventions became more complex (e.g., recurrent incisional hernias 0.5% vs. 1.9%, p < 0.01). The mean length of hospital stay was significantly reduced for incisional hernias (8.8 ± 5.8 vs. 6.7 ± 4.1 days, p < 0.001). The reoperation rate for incisional hernias also decreased significantly from 8.24 to 3.66% (p = 0.04). The postoperative complication rate for inguinal hernias was significantly reduced (3.1 vs. 1.1%, p = 0.002). The reimbursement of the hernia center increased by 27.6%. There were positive changes in process and outcome quality and reimbursement after the certification, which supports the effectivity of certifications in hernia surgery.