We derive the fermion bilinear terms in the world volume action for a D3 brane in the presence of background flux. In six-dimensional compactifications non-perturbative corrections to the superpotential can arise from an euclidean D3-brane instanton wrapping a divisor in the internal space. The bilinear terms give rise to fermion masses and are important in determining these corrections. We find that the three-form flux generically breaks a U(1) subgroup of the structure group of the normal bundle of the divisor. In an example of compactification on T6/Z2, twelve of the sixteen zero modes originally present are lifted by the flux. © SISSA 2005.