The magnetic fields generated in non-central heavy-ion collisions are among the strongest fields produced in the Universe, reaching magnitudes comparable to the scale of the strong interactions. Backed by model simulations, the resulting field is expected to be spatially modulated, deviating significantly from the commonly considered uniform profile. To improve our understanding of the physics of quarks and gluons under such extreme conditions, we use lattice QCD simulations with $2+1$ staggered fermion flavors with physical quark masses and an inhomogeneous magnetic background for a range of temperatures covering the QCD phase transition. We assume a $1/\cosh^2$ function to model the field profile and vary its strength to analyze the impact on the computed observables and on the transition. We calculate local chiral condensates, local Polyakov loops and estimate the size of lattice artifacts. We find that both observables show non-trivial spatial features due to the interplay between the sea and the valence effects.