Nucleic acid drugs hold great promise for potential treatment of a variety of diseases. But efficient delivery is still the major challenge impeding translation. Nanoformulations based on polymers and lipids require preparation processes such as microfluidic mixing, spray drying or final filling, where pumping is a crucial step. Here, we studied the effect of pumping on the com-ponent and overall loss of a binary polyplex formulation made of DNA and polyethyleneimine (PEI). We varied tubing length and material with a focus on subsequent spray drying. Interestingly, product loss increased with the length of silicon tubing. Losses of DNA were prevented by using Pumpsil. The following spray drying process did not affect DNA content but caused PEI loss. Characterization of the different tubing materials revealed similar hydrophobicity of all tubing materials and showed neutral Pumpsil surface charge, negative Santoprene surface charge, and a positive Silicon surface charge. Hence, adsorption of DNA onto tubing material was concluded to be the root cause for DNA loss after pumping and is based upon an interplay of ionic and hydrophobic interactions between polyplexes and tubing material. Overall, selecting the ap-propriate tubing material for processing nucleic acid nanoparticles is key to achieving satisfactory product quality.