Abstract A model with fermion and scalar fields charged under a Peccei–Queen (PQ) symmetry is proposed. The PQ charges are chosen in such a way that they can reproduce mass matrices with five texture zeros, which can generate the fermion masses, the CKM matrix, and the PMNS matrix of the Standard Model (SM). To obtain this result, at least 4 Higgs doublets are needed. As we will see in the manuscript this is a highly non-trivial result since the texture zeros of the mass matrices impose a large number of restrictions. This model shows a route to understand the different scales of the SM by extending it with a multi-Higgs sector and an additional PQ symmetry. Since the PQ charges are not universal, the model predicts flavor-changing neutral currents (FCNC) at the tree level, a feature that constitutes the main source of restrictions on the parameter space. We report the allowed regions by lepton decays and compare them with those coming from the semileptonic decays $$K^{\pm }\longrightarrow \pi {\bar{\nu }}\nu $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msup> <mml:mi>K</mml:mi> <mml:mo>±</mml:mo> </mml:msup> <mml:mo>⟶</mml:mo> <mml:mi>π</mml:mi> <mml:mover> <mml:mrow> <mml:mi>ν</mml:mi> </mml:mrow> <mml:mrow> <mml:mo>¯</mml:mo> </mml:mrow> </mml:mover> <mml:mi>ν</mml:mi> </mml:mrow> </mml:math> . We also show the excluded regions and the projected bounds of future experiments for the axion–photon coupling as a function of the axion mass and compare it with the parameter space of our model.