Empirical Mode Decomposition (EMD) is a technique that converts the measured signal into a number of basic functions known as intrinsic mode functions. The EMD-based damage detection algorithm relies on the principle that a sudden loss of stiffness in a structural member will cause a discontinuity in the measured response that can be detected through a distinctive spike in the filtered intrinsic mode function. Recent studies have shown that applying EMD to the acceleration response, due to the crossing of a constant load over a beam finite element model, can be used to detect a single damaged location. In this paper, the technique is further tested using the response of a discretized finite element beam with multiple damaged sections modeled as localized losses of stiffness. The ability of the algorithm to detect more than one damaged section is analysed for a variety of scenarios including a range of bridge lengths, speeds of the moving load and noise levels. The use of a moving average filter on the acceleration response, prior to applying EMD, is shown to improve the sensitivity to damage. The influence of the number of measurement points and their distance to the damaged sections on the accuracy of the predicted damage is also discussed.