In guided wave structural health monitoring, defects are typically detected by identifying high residuals obtained via the baseline subtraction method, where an earlier measurement is subtracted from the ‘current’ signal. Unfortunately, varying environmental and operational conditions, such as temperature, also produce signal changes and hence, potentially, high residuals. While the majority of the temperature compensation methods that have been developed target the changed wave speed induced by varying temperature, a number of other effects are not addressed, such as changes in attenuation, the relative amplitudes of different modes excited by the transducer and the transducer frequency response. A temperature compensation procedure is developed whose goal is to correct any spatially dependent signal change that is a systematic function of temperature. At each structural position, a calibration function that models the signal variation with temperature is computed and is used to correct the measurements, so that in the absence of a defect the residual is reduced to close to zero. This new method was applied to a set of guided wave signals collected in a blind trial of a guided wave pipe monitoring system employing the T(0,1) mode, yielding residuals de-coupled from temperature and reduced by at least 50% compared to those obtained using the standard approach at positions away from structural features, and by more than 90% at features such as the pipe end. The method therefore promises a substantial improvement in the detectability of small defects, particularly at existing pipe features.