We investigate Majorana dark matter in a new variant of $U(1)_{L_{mu}-L_{tau}}$ gauge extension of Standard Model, containing three additional neutral fermions $N_{e}, N_{mu}, N_{tau}$, along with a $(bar{3},1,1/3)$ scalar Leptoquark (SLQ) and an inert doublet, to study the phenomenology of dark matter, neutrino mass generation and flavour anomalies on a single platform. The lightest mass eigenstate of the $N_{mu}, N_{tau}$ neutral fermions plays the role of dark matter. We compute the WIMP-nucleon cross section in leptoquark portal and the relic density mediated by inert doublet components, leptoquark and the new $Z^{prime}$ boson. We constrain the parameter space consistent with Planck limit on relic density, PICO-60 and LUX bounds on spin-dependent direct detection cross section. We also discuss about the neutrino mass generation at one-loop level and the viable parameter region to explain current neutrino oscillation data. The $Z^prime$ gauge boson of extended $U(1)$ symmetry and the SLQ play an important role in settling the known issues of flavor sector.