Periprosthetic infections (PPIs) are a serious concern in total knee and hip arthroplasty, and they have an increasing incidence. To prevent PPI, preoperative skin disinfection, as a key element of antisepsis, represents an important part of infection prevention. However, no specific antiseptic agent is endorsed by the relevant guidelines. The purpose of this retrospective, not randomized study was to investigate the difference in the residual bacteria load between an approved antiseptic with an alcohol-based solution with additional benzalkonium chloride (BAC) and an alcohol-based solution with additional octenidine dihydrochloride (OCT) at two different time periods. In 200 consecutive patients with total knee or hip arthroplasty, skin samples from the surgical sites were collected after skin disinfection with BAC (100 g solution contain: propan-2-ol 63.0 g, benzalkonium chloride 0.025 g) or OCT (100 g solution contain: octenidine dihydrochloride 0.1 g, propan-1-ol, 30.0 g, propan-2-ol 45.0 g) (100 patients per group). Following the separation of cutis and subcutis and its processing, culture was performed on different agar plates in aerobic and anaerobic environments. In the case of bacteria detection, the microbial identification was determined by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and the number of contaminated samples was compared between the groups. Additionally, multiple regression analysis was performed to examine the effect of the type of disinfectant, BMI, age, sex, rheumatoid arthritis, diabetes mellitus, skin disorders, smoking status, and localization of skin samples on positive bacteria detection. A total of 34 samples were positive for bacteria in the BAC group, while only 17 samples were positive in the OCT group (p = 0.005). Disinfectant type was the only significant parameter in the multiple regression analysis (p = 0.006). A significantly higher contamination rate of the subcutis was shown in the BAC group compared to the OCT group (19 vs. 9, p = 0,003). After the change from BAC to OCT in preoperative skin cleansing in the hip and knee areas, the number of positive cultures decreased by 50%, which might have been caused by a higher microbicidal activity of OCT. Therefore, the use of OCT in preoperative cleansing may reduce the risk of PPI in hip and knee surgery. Randomized controlled trials are required to confirm the effect and to evaluate if it reduces the risk of PPI.