The enzymatic activity of glucosylceramidase depends on the presence of saposin C (Sap C) and acidic phospholipid-containing membranes. In order to delineate the mechanism underlying Sap C stimulation of the enzyme activity, it is important to understand how Sap C interacts with phospholipid membranes. We studied the dynamic process of Sap C interaction with planar phospholipid membranes, in real time, using atomic force microscopy (AFM). The phospholipid membrane underwent restructuring upon addition of Sap C. The topographic characteristics of the membrane restructuring include the appearance of patch-like new features, initially emerged at the edge of phospholipid membranes and extended laterally with time. Changes in the image contrast of the phospholipid membrane observed after the Sap C addition indicate that a new phase of lipid-protein structure has formed during membrane restructuring. The process of membrane restructuring is dynamic, commencing shortly after Sap C addition, and continuing throughout the duration of AFM imaging (about 30 min, sometimes over 1 h). This study demonstrated the potential of AFM real-time imaging in studying protein-membrane interactions.