The present study investigates Joule heating in piezoresistive microcantilever sensors. Joule heating and thermal deflections are a major source of noise in such sensors. This work uses analytical and numerical techniques to characterise the Joule heating in 4-layer piezoresistive microcantilevers made of silicon and silicon dioxide substrates but with the same U-shaped silicon piezoresistor. A theoretical model for predicting the temperature generated due to Joule heating is developed. The commercial finite element software ANSYS Multiphysics was used to study the effect of electrical potential on temperature and deflection produced in the cantilevers. The effect of piezoresistor width on Joule heating is also studied. Results show that Joule heating strongly depends on the applied potential and width of piezoresistor and that a silicon substrate cantilever has better thermal characteristics than a silicon dioxide cantilever.