A method of controlling polishing includes polishing a stack of adjacent conductive layers on a substrate, measuring with an in-situ eddy current monitoring system a sequence of characterizing values for the substrate during polishing, calculating a polishing rate from the sequence of characterizing values repeatedly during polishing, calculating one or more adjustments for one or more polishing parameters based on a current polishing rate using a first control algorithm for an initial time period, detecting a change in the polishing rate that indicates exposure of the underlying conductive layer, and calculating one or more adjustments for one or more polishing parameters based on the polishing rate using a different second control algorithm for a subsequent time period after detecting the change in the polishing rate.