We demonstrate three-dimensional magnetic resonance tomography with a resolution down to 5.9 ± 0.1 nm. Our measurements use lithographically fabricated microwires as a source of three-dimensional magnetic field gradients, which we use to image NV centers in a densely doped diamond by Fourier-accelerated magnetic resonance tomography. We also demonstrate a compressed sensing scheme, which allows for direct visual interpretation without numerical optimization and implements an effective zoom into a spatially localized volume of interest, such as a localized cluster of NV centers. It is based on aliasing induced by equidistant undersampling of k-space. The resolution achieved in our work is comparable to the best existing schemes of super-resolution microscopy and approaches the positioning accuracy of site-directed spin labeling, paving the way to three-dimensional structure analysis by magnetic-gradient based tomography.