We present a study of the isospin-breaking (IB) corrections to pseudoscalar (PS) meson masses using the gauge configurations produced by the ETM Collaboration with $N_f=2+1+1$ dynamical quarks at three lattice spacings varying from 0.089 to 0.062 fm. Our method is based on a combined expansion of the path integral in powers of the small parameters $(widehat{m}_d - widehat{m}_u)/Lambda_{QCD}$ and $alpha_{em}$, where $widehat{m}_f$ is the renormalized quark mass and $alpha_{em}$ the renormalized fine structure constant. We obtain results for the pion, kaon and $D$-meson mass splitting; for the Dashens theorem violation parameters $epsilon_gamma(overline{mathrm{MS}}, 2~mbox{GeV})$, $epsilon_{pi^0}$, $epsilon_{K^0}(overline{mathrm{MS}}, 2~mbox{GeV})$; for the light quark masses $(widehat{m}_d - widehat{m}_u)(overline{mathrm{MS}}, 2~mbox{GeV})$, $(widehat{m}_u / widehat{m}_d)(overline{mathrm{MS}}, 2~mbox{GeV})$; for the flavour symmetry breaking parameters $R(overline{mathrm{MS}}, 2~mbox{GeV})$ and $Q(overline{mathrm{MS}}, 2~mbox{GeV})$ and for the strong IB effects on the kaon decay constants.