We calculate non-perturbative contributions to Yukawa couplings on D3-branes at orbifold singularities due to E3 and fractional E(-1) instantons which do not intersect the visible sector branes. While distant E3 instantons on bulk cycles typically contribute to Yukawa couplings, we find that distant fractional E(-1) can also give rise to new Yukawa couplings. However, fractional E(-1) instantons only induce Yukawa couplings if they are located at a singularity which shares a collapsed homologous two-cycle with the singularity supporting the visible sector. The non-perturbative contributions to Yukawa couplings exhibit a different flavour structure than the tree-level Yukawa couplings and, as a result, they can be sources of flavour violation. This is particularly relevant for schemes of moduli stabilisation which rely on superpotential contributions from E3 instantons, such as KKLT or the Large Volume Scenario. As a byproduct of our analysis, we shed some new light on the properties of annulus diagrams with matter field insertions in stringy instanton calculus.