alpha,omega-Dicarboxylic acids (DC) are versatile chemical intermediates with different chain length. For biosynthesis of DC, to obtain the highly pure product via crystallization, it is required to remove pigments and proteins in fermentation broth. However, a trade-off between decolorization/deproteinization ratio and DC recovery during the purification process was found, which impeded DC production by fermentation. When ultrafiltration (UF) was applied to treat alpha,omega-dodecanedioic acid (DC12) broth, 93.4% of DC12 recovery, 80.5% of decolorization ratio and 61.7% of deproteinization ratio were achieved by a PES 3 membrane. However, the membrane technology could not effectively retain the pigments or proteins with low molecular weight when a high DC12 permeation was required. Meanwhile, the selected activated charcoal or macroporous resins were not good adsorbents for the present system. Furthermore, an integrated process for decolorization and deproteinization was developed. After filtration with PES3 membrane, an activated charcoal was used to remove the small proteins and pigments in the UF permeate. As a result, 91.4% of DC12 recovery, 94.7% of decolorization ratio and 84.8% of deproteinization ratio were obtained by such two-stage strategy. These results would serve as a valuable guide for process design and practical operation in subsequent industrial application.