The extension of Standard Model made by inclusion of additional U(1) gauge Lμ-Lτ symmetry can explain the difference between the measured and the predicted value of the muon magnetic moment and solve the tension in B meson decays. This model predicts the existence of a new, light Z′ vector boson, predominantly coupled to second and third generation leptons, whose interaction with electrons is due to a loop mechanism involving muons and taus. In this work, we present a rigorous evaluation of the upper limits in the Z′ parameter space, obtained from the analysis of the data collected by the NA64-e experiment at CERN SPS, that performed a search for light dark matter with 2.84×1011 electrons impinging with 100 GeV on an active thick target. The resulting limits touch the muon g-2 preferred band for values of the Z′ mass of order of 1 MeV, while the sensitivity projections for the future high-statistics NA64-e runs demonstrate the power of the electrons/positron beam approach in this theoretical scenario. The extension of Standard Model made by inclusion of additional $U(1)$ gauge $L_\mu-L_\tau$ symmetry can explain the difference between the measured and the predicted value of the muon magnetic moment and solve the tension in $B$ meson decays. This model predicts the existence of a new, light $Z^\prime$ vector boson, predominantly coupled to second and third generation leptons, whose interaction with electrons is due to a loop mechanism involving muons and taus. In this work, we present a rigorous evaluation of the upper limits in the $Z^\prime$ parameter space, obtained from the analysis of the data collected by the NA64-$e$ experiment at CERN SPS, that performed a search for light dark matter with $2.84\times10^{11}$ electrons impinging with 100 GeV on an active thick target. The resulting limits, despite being included in a region already investigated by neutrino experiments,touch the muon $g-2$ preferred band for values of the $Z^\prime$ mass of order of 1 MeV. The sensitivity projections for the future high-statistics NA64-$e$ runs demonstrate the power of the electrons/positron beam approach in this theoretical scenario.