Axion models with generation-dependent Peccei-Quinn charges can lead to flavor-changing neutral currents, thus motivating QCD axion searches at precision flavor experiments. We rigorously derive limits on the most general effective flavor-violating couplings from current measurements and assess their discovery potential. For two-body decays we use available experimental data to derive limits on $qto q a$ decay rates for all flavor transitions. Axion contributions to neutral-meson mixing are calculated in a systematic way using chiral perturbation theory and operator product expansion. We also discuss in detail baryonic decays and three-body meson decays, which can lead to the best search strategies for some of the couplings. For instance, a strong limit on the $Lambdato n a$ transition can be derived from the supernova SN 1987A. In the near future, dedicated searches for $qto q a$ decays at ongoing experiments could potentially test Peccei-Quinn breaking scales up to $10^{12}$ GeV at NA62 or KOTO, and up to $10^{9}$ GeV at Belle II or BES III.
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