Real-time tracking of dynamic nanoscale processes such as phase transitions by scanning probe microscopy (SPM) is a challenging task, typically requiring extensive and laborious human supervision. Smart strategies to track specific regions of interest (ROI) in the system during such transformations in a fast and automated manner are necessary to study the evolution of the microscopic changes in such dynamic systems. In this work, we realize automated ROI tracking in piezoresponse force microscopy (PFM) during a fast (≈0.8°C/s) thermally stimulated ferroelectric-to-paraelectric phase transition in CuInP2S6. We use a combination of fast (1 frame per second) sparse scanning with compressed sensing image reconstruction and real-time offset correction via phase cross correlation. The applied methodology enables in-situ fast and automated functional nanoscale characterization of a certain ROI during external stimulation that generates sample drift and changes local functionality.