Abstract Background Surgical site infections (SSI) are rare but severe complications after total joint arthroplasty (TJA). Decolonization measures prior to elective orthopedic surgeries have shown to reduce the risk of SSI with Staphylococcus aureus (S. aureus). Objective To determine the efficacy of universal decolonization with Polyhexanide on SSI rates with a focus on Staphylococcus aureus in patients with TJA. Methods Patients scheduled for elective hip or knee TJA in 5 participating certified orthopedic centers were included between 2015 and 2018 into this before and after study. Data on patients, surgeries and infections were prospectively collected. CDC-criteria were used to define and categorize Infections within 90 days after surgery. From January 2017 on, patients received decolonization sets containing Polyhexanide. Patients performed a 5 day decolonization regimen starting 4 days prior to surgery which included wipes, nasal decontamination and oral solution. Results Thirteen thousand, three hundred fifteen patients received TJA. During intervention 4437 decolonization sets were distributed among 7175 patients. Overall SSI rates increased from 0.68 /100 surgeries to 0.91/ 100 surgeries after implementation of the intervention (IRR 1.32; 95% CI 0.90–1.96). Time series analysis identified an increasing trend of SSI prior to the intervention. After implementation overall SSI rates plateaued. Regression analysis revealed surgery during intervention period to be an independent risk factor for developing a SSI (OR 1.34; 95%CI 1.18–1.53). Initial SSI rates due to S. aureus were 0.24/100 surgeries and decreased to 0.14/100 surgeries (IRR 0.57; 95% CI 0.25–1.22) after introduction of decolonization. Regression analysis revealed surgery during intervention period to be an independent protective factor for developing a SSI with S. aureus (OR 0.57, 95% CI: 0.33–0.99). Overall deep S. aureus SSI decreased significantly from 0.22/100 surgeries to 0.00/100 surgeries in patients adherent to protocol (IRR 0.00, 95% CI 0.00–.85). Conclusion Universal decolonization with Polyhexanide did not reduce overall surgical site infections, but was effective in reducing Staphylococcus aureus - surgical site infections following elective joint arthroplasty. Polyhexanide could extend the list of alternatives to already established decolonization strategies. Trial registration The trial was registered at the German Registry for clinical studies www.drks.de (DRKS00011505).