Atomic force microscopy is employed to study the influence of the motion of a glycerol solution through a coiled (spiral-wound) polymeric communication pipe on the aggregation state of a protein, with the example of a horseradish peroxidase (HRP) enzyme. The measuring cell with the buffered solution of the protein was placed within the experimental setup over the pipe coil, through which glycerol was pumped. It is demonstrated that, in such a system, the flow of a non-aqueous liquid (glycerol) leads to a change in the physicochemical properties of a protein, whose solution was incubated in the measuring cell placed over the coil. Namely, changes in both the adsorbability onto mica and the aggregation state of the model HRP protein were observed. As glycerol-containing liquids are commonly used in biosensor operations, the results reported herein can be useful to the development of biosensor systems, in which polymeric communications are employed in sample delivery and thermal stabilization systems. The data obtained herein can also be of use for the development of specified hydrodynamic models.