Most of the anomalies in flavor physics (both old and new) are associated with processes that are affected by non-perturbative aspects of QCD. At the precision level, the theory is generally complicated by second-order electroweak corrections which resolve the substructure of the decaying hadron. In this talk I will present an overview of the phenomenological importance, and the (effective field theory) tools and methods used to calculate hadronic substructure corrections to leptonic and semileptonic decays of mesons, with an emphasis on ongoing work in $K^+ \to \pi^+ \nu \bar{\nu}$, $D_s \to \tau \nu$ and $B \to X_s \nu \bar{\nu}$ decays.