Integrated forest biorefinery offers promising pathways to sustainably diversify the revenue of pulp and paper industry. In this context, lignin can be extracted from a residual stream of Kraft pulping process, called black liquor, and subsequently converted into a wide spectrum of bio-based products. Electrochemical acidification of Kraft black liquor by electrodialysis with bipolar membrane results in lignin extraction and caustic soda production. Even though the implementation of this method requires less chemicals than the chemical acidification process, fouling of the ion exchange membranes and especially bipolar membrane impairs its productivity. Membrane thickness and ash content measurements along with scanning electron microscopy (SEM), elemental analysis (EDX) and X-ray photoelectron spectrometry (XPS) analysis were performed to identify the nature and mechanisms of the membrane fouling. The results revealed that the fouling layer mostly consisted of organic components and particularly lignin. Based on our proposed fouling mechanisms, throughout the electrodialysis process the pH of the black liquor gradually decreased and as a result more proton ions were available to trigger protonation reaction of lignin phenolic groups and decrease the lignin solubility. Due to the abundance of the proton ions on the surface of the cation exchange layers of the bipolar membrane, destabilized lignin macro-molecules started to self-aggregate and formed lignin clusters on its surface. Over the time, these lignin clusters covered the entire surface of the bipolar membrane and the spaces between the membranes and, eventually, attached to the surface of the cation exchange membrane.