We describe the microphysics, phenomenology, and astrophysical implication of a B-field induced unpairing effect that may occur in magnetars, if the local B field in the core of a magnetar exceeds a critical value Hc2. Using the Ginzburg-Landau theory of superconductivity, we derive the Hc2 field for proton condensate taking into the correction (≤30%) which arises from its coupling to the background neutron condensate. The density dependence of pairing of proton condensate implies that Hc2 is maximal at the crust-core interface and decreases towards the center of the star. As a consequence, magnetar cores with homogenous constant fields will be partially superconducting for "medium-field" magnetars (1015≤B≤5×1016G) whereas "strong-field" magnetars (B>5×1016G) will be void of superconductivity. The neutrino emissivity of a magnetar's core changes in a twofold manner: (i) the B-field assisted direct Urca process is enhanced by orders of magnitude, because of the unpairing effect in regions where B≥Hc2; (ii) the Cooper-pair breaking processes on protons vanish in these regions and the overall emissivity by the pair-breaking processes is reduced by a factor of only a few. © 2015 American Physical Society.