Microfiltration (MF) and ultrafiltration (UF) membranes were screened for improving the specific activity of polygalacturonases (PG) in the culture broth of Aspergillus carbonarius obtained after submerged fermentation. While 200 and 450 nm MF membranes eliminated some of the larger non-enzymatic proteins, 50 kDa UF membrane exhibited a marginal selectivity between the enzyme and other smaller proteins. The 450 nm MF and 50 kDa UF membranes selected were further evaluated under different process conditions for an integrated membrane process. The process efficacy of three different schemes was also studied for enzyme purification. A two-stage membrane process employing MF followed by UF improved the enzyme-specific activity (5,590 U/mg) by 4.69-fold eliminating the larger and smaller non-enzymatic proteins as well as non-protein impurities with a recovery of 76% enzymes, besides resulting in higher productivity. Thus, adoption of integrated membrane process with appropriate selection of membranes could result in high recovery of enzymes with improved specific activity.