We perform a complete study of the low-energy phenomenology of $S_1$ and $S_3$ lepto-quarks, aimed at addressing the observed deviations in $B$-meson decays and the muon magnetic dipole moment. Leptoquark contributions to observables are computed at one-loop accuracy in an effective field theory approach, using the recently published complete one-loop matching of these leptoquarks to the Standard Model effective field theory. We present several scenarios, discussing in each case the preferred parameter space and the most relevant observables.