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A two\u2010step ATPS using polyethylene glycol (PEG) and sodium citrate that recovered 66% of infectious porcine parvovirus with 2.0 logs of protein removal and 1.0 logs of DNA removal in batch has now been run continuously. The continuous system output of &lt;10\u2009ng\/mL DNA regardless of starting DNA titer agreed with batch studies. However, the continuous system had a five\u2010fold higher contaminating protein titer than batch studies, likely because of incomplete mixing or settling. Turbidity was tested as a measure of mixing and settling efficiency. Monitoring in\u2010line absorbance at 880\u2009nm directly after mixing and before collection in the settling reservoir could track both mixing and settling during operation. Settling time was reduced by changing the settling line material from PVC to PTFE, which is more hydrophobic. A flow\u2010through AEX filter tested to make impurity removal more robust recovered 90% of PPV and removed an additional 87% of host cell DNA. The filter did not add any additional protein removal. In the future, in\u2010line absorbance sensors could be implemented along with conductivity sensors to measure salt concentration, refractive index sensors to track the PEG\u2010citrate interface, and scales to track mixer and reservoir volumes to enable automated, continuous ATPS. 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