Quantum gas microscopes probe quantum many-body lattice states via projective measurements in the occupation basis, enabling access to various density and spin correlations. Phase information, however, cannot be directly obtained in these setups. Recent experiments went beyond this by measuring local current operators and local phase fluctuations. Here we propose how Fourier-space manipulation in a matter-wave microscope allows access to various long-range off-diagonal correlators in experimentally realistic settings, realizing a many-body phase microscope. We demonstrate in particular how the fermionic d-wave superconducting order parameter in arbitrary Hubbard-type models, the non-equal time Green’s function yielding the spectral function, or the hidden order of composite bosons in a fractional Chern insulator can be directly measured. Our results show the great potential of matter-wave microscopy for accessing exotic correlators including phases and coherences and characterizing intriguing quantum many-body states.