  Closed string fluxes induce generically SUSY-breaking soft terms on
supersymmetric type IIB orientifold compactifications with D3/D7 branes. This
was studied in the past by inserting those fluxes on the DBI+CS actions for
adjoint D3/D7 fields, where D7-branes had no magnetic fluxes. In the present
work we generalise those computations to the phenomenologically more relevant
case of chiral bi-fundamental fields laying at 7-brane intersections and
F-theory local matter curves. We also include the effect of 7-brane magnetic
flux as well as more general closed string backgrounds, including the effect of
distant (anti-)D3-branes. We discuss several applications of our results. We
find that squark/slepton masses become in general flux-dependent in F-theory
GUT's. Hypercharge-dependent non-universal scalar masses with a characteristic
sfermion hierarchy m_E^2 < m_L^2 < m_Q^2 < m_D^2 < m_U^2 are obtained. There
are also flavor-violating soft terms both for matter fields living at
intersecting 7-branes or on D3-branes at singularities. They point at a very
heavy sfermion spectrum to avoid FCNC constraints. We also discuss the possible
microscopic description of the fine-tuning of the EW Higgs boson in
compactifications with a MSSM spectrum.
