During biopharmaceutical production, efficient removal of impurities via filtration is essential. It is desirable to achieve high filter capacities along with a high degree of clearance. However, the complexity of bacterial cell lysates makes it difficult to properly estimate the filtration behavior. Here we investigated how host cell-derived impurities impacted the performance of commercially available sterile filters, with a focus on characterizing the dsDNA-induced decrease of filter capacity. Pressure flow curves at a constant flow, combined with particle analytics (e.g., nanoparticle-tracking analysis), indirectly revealed that dsDNA had a major influence on rapid membrane fouling. The observed phenomenon was more pronounced when using filters with small pore sizes (<0.2 µm). Filter capacity could be substantially increased by reducing the size of the present dsDNA fragments, or by decreasing the potential for dsDNA-driven electrostatic interactions with positively charged molecules. In general, our present findings highlight the importance of monitoring dsDNA even during the primary recovery of proteins in cell lysates.