The color neutral two-flavor superconducting (2SC) phase of cold and dense quark matter is studied in the presence of constant magnetic fields and at moderate baryon densities. In the first part of the paper, a two-flavor effective Nambu-Jona-Lasinio (NJL) model consisting of a chiral symmetry breaking (χSB) mass gap σ B , a color superconducting (CSC) mass gap ∆ B and a color chemical potential µ 8 is introduced in the presence of a rotated U (1) magnetic field B. To study the phenomenon of magnetic catalysis in the presence of strong magnetic fields, the gap equations corresponding to σ B and ∆ B , as well as µ 8 are solved in the lowest Landau level (LLL) approximation. In the second part of the paper, a detailed numerical analysis is performed to explore the effect of any arbitrary magnetic field on the above mass gaps and the color chemical potential. The structure of the χSB and CSC phases is also presented in the µ c − ẽB plane, and the effect of µ 8 on the phase structure of the model is explored. As it turns out, whereas the transition from the χSB to CSC phase is of first order, nonvanishing µ 8 affects essentially the second order phase transition from CSC to the normal phase.