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Abstract The effects of strong magnetic fields on the deconfinement phase transition expected to take place in the interior of massive neutron stars are studied in detail for the first time. For hadronic matter, the very general density-dependent relativistic mean field model is employed, while the simple, but effective vector-enhanced bag model is used to study quark matter. Magnetic-field effects are incorporated into the matter equation of state and in the general-relativity solutions, which also satisfy Maxwell’s equations. We find that for large values of magnetic dipole moment, the maximum mass, canonical mass radius, and dimensionless tidal deformability obtained for stars using spherically symmetric Tolman–Oppenheimer–Volkoff (TOV) equations and axisymmetric solutions attained through the LORENE library differ considerably. The deviations depend on the stiffness of the equation of state and on the star mass being analyzed. This points to the fact that, unlike what was assumed previously in the literature, magnetic field thresholds for the approximation of isotropic stars and the acceptable use of TOV equations depend on the matter composition and interactions.