AbstractQuantum metrology overcomes standard precision limits by exploiting collective quantum superpositions of physical systems used for sensing, with the prominent example of non-classical multiphoton states improving interferometric techniques. Practical quantum-enhanced interferometry is, however, vulnerable to imperfections such as partial distinguishability of interfering photons. Here we introduce a method where appropriate design of the modal structure of input photons can alleviate deleterious effects caused by another, experimentally inaccessible degree of freedom. This result is accompanied by a laboratory demonstration that a suitable choice of spatial modes combined with position-resolved coincidence detection restores entanglement-enhanced precision in the full operating range of a realistic two-photon Mach–Zehnder interferometer, specifically around a point which otherwise does not even attain the shot-noise limit due to the presence of residual distinguishing information in the spectral degree of freedom. Our method highlights the potential of engineering multimode physical systems in metrologic applications.