A monoclonal antibody drug product (DP) manufacturing process was transferred to a different production site, where aseptic filling took place within an isolator that was sanitized using vapor phase hydrogen peroxide (VPHP). A quality-by-design approach was applied for study design to understand the impact of VPHP uptake in the isolator on DP quality. A combination of small-scale and manufacturing-scale studies was performed to evaluate the sensitivity of the monoclonal antibody to hydrogen peroxide (H2O2) as well as VPHP uptake mechanisms during the filling process. The acceptable H2O2 level was determined to be 100 ng/mL for the antibody in the H2O2 spiking study; protein oxidation was observed above this threshold. The most prominent sources of VPHP uptake were identified to be via the silicone tubing assembly (associated with the peristaltic pumps) and open, filled vials. Silicone tubing, an effective depot to H2O2, could absorb VPHP during different stages of the filling process and discharge H2O2 into the DP solution during filling interruptions. A small-scale isolator model, established to simulate manufacturing-scale conditions, was a useful tool in understanding H2O2 uptake in relation to tubing dimensions and VPHP concentration in the isolator air (or atmosphere). Although the tubing assembly had absorbed a substantial amount of VPHP during the decontamination phase, the majority of H2O2 could be removed during tubing cleaning and sterilization in the subsequent isolator aeration phase, demonstrating that H2O2 in the DP solution is taken up primarily via atmospheric VPHP residues in the isolator during filling. Picarro sensor monitoring suggested that the validated VPHP aeration process generates reproducible residual VPHP profiles in isolator air, thus allowing small-scale studies to provide more relevant recommendations on tubing size and interruption time limits for commercial manufacturing. The recommended process parameters were demonstrated to be acceptable and rendered no product quality impact as demonstrated in six consecutive manufacturing batches in the process validation campaign. Overall, this case study would provide process development scientists/engineers an in-depth understanding of the VPHP process and a science-based approach to mitigating DP quality impact.