We present the performance of multiplexed XY resistive Micromegas detectors tested in the CERN SPS 100 GeV/c electron beam at intensities up to 3.3 $times$ 10$^5$ e$^- $/(s$cdot$cm$^2$). So far, all studies with multiplexed Micromegas have only been reported for tests with radioactive sources and cosmic rays. The use of multiplexed modules in high intensity environments was not explored due to the effect of ambiguities in the reconstruction of the hit point caused by the multiplexing feature. At the beam intensities analysed in this work and with a multiplexing factor of 5, more than 50% level of ambiguity is introduced. Our results prove that by using the additional information of cluster size and integrated charge from the signal clusters induced on the XY strips, the ambiguities can be reduced to a level below 2%. The tested detectors are used in the CERN NA64 experiment for tracking the incoming particles bending in a magnetic field in order to reconstruct their momentum. The average hit detection efficiency of each module was found to be $sim$ 96% at the highest beam intensities. By using four modules a tracking resolution of 1.1% was obtained with $sim$ 85% combined tracking efficiency.