(1) Background: Surgical site skin preparation is an important approach to prevent postoperative wound infections. International guidelines recommend that alcohol-based combinations be used, however, the optimal combination remains uncertain. This study compares the effectiveness of alcohol-based chlorhexidine and alcohol-based iodophor for surgical site skin preparation for prevention of surgical site infections (SSIs). (2) Methods: Randomised controlled trials comparing alcohol-based interventions for surgical site skin preparation were included. The proportion of SSIs was compared using risk ratios (RR) with 95% confidence intervals (95% CI). The meta-analysis was performed with a fixed effect model using Mantel-Haenszel methods. As an a priori subgroup analysis SSI risk was examined according to different surgical procedural groups. (3) Results: Thirteen studies were included (n = 6023 participants). The use of chlorhexidine-alcohol was associated with a reduction in risk of SSIs compared with iodophor-alcohol (RR 0.790; 95% CI 0.669, 0.932). On sub-group analysis, chlorhexidine-alcohol was associated with a reduction in SSIs in caesarean surgery (RR 0.614; 95% CI 0.453, 0.831) however, chlorhexidine-alcohol was associated with an increased risk of SSI in bone and joint surgery (RR 2.667; 95% CI 1.051, 6.765). When excluding studies at high risk of bias on sensitivity analysis, this difference in alcohol-based combinations for bone and joint surgery was no longer observed (RR 2.636; 95% CI 0.995, 6.983). (4) Conclusions: The use of chlorhexidine-alcohol skin preparations was associated with a reduced risk of SSI compared to iodophor-alcohol agents. However, the efficacy of alcohol-based preparation agents may differ according to the surgical procedure group. This difference must be interpreted with caution given the low number of studies and potential for bias, however, it warrants further investigation into the potential biological and clinical validity of these findings.