Meson mixing is considered to be an ideal testing ground for new physics searches. Experimental precision has greatly increased over the recent years, exceeding in several cases the theoretical precision. A possible limit in the theoretical accuracy could be a hypothetical breakdown of quark-hadron duality. We propose a simple model for duality violations and give stringent bounds on its effects on mixing observables, indicating regions where future measurements of $\Delta\Gamma_d$, $a_{sl}^d$ and $a_{sl}^s$ would give clear signals of new physics. Finally, we turn our attention to the charm sector, and reveal that a modest duality violation of about 20% could explain the huge difference between HQE predictions for D-mixing and experimental data.