Half-integer quantized flux vortices appear in honeycomb lattices when the signs of an odd number of couplings around a plaquette are inverted. We show that states trapped at these vortices can be isolated by applying inhomogeneous strain to the system. A vortex then results in localized midgap states lying between the strain-induced pseudo-Landau levels, with 2n+1midgap states appearing between the nth and the (n+1)th level. These states are well-defined spectrally isolated and spatially localized excitations that could be realized in electronic and photonic systems based on graphenelike honeycomb lattices. In the context of Kitaev's honeycomb model of interacting spins, the mechanism improves the localization of non-Abelian anyons in the spin-liquid phase, and reduces their mutual interactions. The described states also serve as a testbed for fundamental physics in the emerging low-energy theory, as the correct energies and degeneracies of the excitations are only replicated if one accounts for the effective hyperbolic geometry induced by the strain. We further illuminate this by considering the effects of an additional external magnetic field, resulting in a characteristic spatial dependence that directly maps out the inhomogeneous metric of the emerging hyperbolic space.