Significant loss of preservative was observed during filling of drug products during filling line stops. This study evaluated the losses of three commonly used preservatives in protein drugs, i.e. benzyl alcohol, phenol, and m-cresol. Concentration losses during static incubation were quantified and interpreted with regard to the potential driving forces for the underlying sorption, diffusion, and desorption steps. Partitioning from the solution into the silicone polymer was identified as the most decisive parameter for the extent of preservative loss. Additionally, the influence of tubing inner diameter, starting concentration as well as silicone tubing type was evaluated. Theoretical calculations assuming equilibrium between solution and tubing inner surface and one-directional diffusion following Fick’s first law were used to approximate experimental data. Since significant losses were found already after few minutes, adequate measures must be taken to avoid deviations during filling of preservative-containing protein solutions that may impact product quality or antimicrobial efficacy. As a possible alternative to the highly permeable silicone tubing, a specific make of fluoropolymer tubing was identified being suitable for peristaltic pumps and not showing any preservative losses.