We study the effect of RR and NSNS 3-form fluxes on the effective action of the world-volume fields of Type IIB D7/D3 brane configurations. The D7-branes wrap 4-cycles Σ 4 on a local Calabi–Yau geometry. This is an extension of previous work on hep-th/0311241, where a similar analysis was applied to the case of D3-branes. Our present analysis is based on the D7- and D3-brane Dirac–Born–Infeld and Chern–Simons actions, and makes full use of the R-symmetries of the system, which allow us to compute explicitly results for the fields lying at the D3–D7 intersections. A number of interesting new properties appear as compared to the simpler case of configurations with only D3-branes. As a general result one finds that fluxes stabilize some or all of the D7-brane moduli. We argue that this is important for the problem of stabilizing Kähler moduli through non-perturbative effects in KKLT-like vacua. We also show that ( 0 , 3 ) imaginary self-dual fluxes, which lead to compactifications with zero vacuum energy, give rise to SUSY-breaking soft terms including gaugino and scalar masses, and trilinear terms. Particular examples of chiral MSSM-like models of this class of vacua, based on D3–D7 brane systems at orbifold singularities are presented.