Leptoquarks provide viable solutions to the flavour anomalies, i.e. they can explain the tensions between the measurements and the Standard Model predictions of the anomalous magnetic moment of the muon as well as b → sℓ⁺ℓ⁻ and b → cτν processes. However, LQs also contribute to other flavour observables, such as ∆F = 2 processes, at the loop-level. In particular, B_s−B¯ _s mixing provides a crucial bound in setups addressing b → cτν data, often excluding a big portion of the parameter space that could otherwise account for it. In this article, we first derive the complete leading order matching, including all five scalar LQ representations, for D⁰−D¯ ⁰, K⁰−K¯ ⁰ and B_s,d−B¯ _s,d mixing (at the dimension-six level). We then calculate the next-to-leading order α_s matching corrections to these ∆F = 2 processes in generic scalar leptoquark models. We find that the two-loop corrections increase the effects in ∆F = 2 processes by ~ 5-10% and significantly reduce the matching scale uncertainty.