A multiplicity of quark-lepton families can naturally arise as zero-modes in flux compactifications. The flavour structure of quark and lepton mass matrices is then determined by the wave function profiles of the zero-modes. We consider a supersymmetric $SO(10)\times U(1)$ model in six dimensions compactified on the orbifold $T^2/{\mathbb Z_2}$ with Abelian magnetic flux. A bulk $\mathbf{16}$-plet charged under the $U(1)$ provides the quark-lepton generations whereas two uncharged $\mathbf{10}$-plets yield two Higgs doublets. Bulk anomaly cancellation requires the presence of additional $\mathbf{16}$- and $\mathbf{10}$-plets. The corresponding zero-modes form vectorlike split multiplets that are needed to obtain a successful flavour phenomenology. We analyze the pattern of flavour mixings for the two heaviest families of the Standard Model and discuss possible generalizations to three and more generations.