Haughton is a ~24 Myr old mid-size (apparent diameter 23 km) complex impact structure located on Devon Island in Nunavut, Canada. The center of the structure shows a negative gravity anomaly of -12 mgal coupled to a localized positive magnetic field anomaly of ~900 nT. A field expedition in 2013 led to the acquisition of new ground magnetic field mapping and electrical resistivity datasets, as well as the first subsurface drill cores down to 13 m depth at the top of the magnetic field anomaly. Petrography, rock magnetic and petrophysical measurements were performed on the cores and revealed two different types of clast-rich polymict impactites: (1) a white hydrothermally-altered impact breccia, not previously observed at Haughton, and (2) a grey impact breccia with no macroscopic sign of alteration. In the altered core, gypsum is present in macroscopic veins and in the form of intergranular selenite associated with colored and zoned carbonate clasts. This altered core has a natural remanent magnetization (NRM) four to five times higher than materials from the other core but the same magnetic susceptibility. Their magnetization is still higher than the surrounding crater-fill impact melt rocks. X-ray Fluorescence data indicate a similar proportion of iron-rich phases in both cores and an enrichment in silicates within the altered core. In addition, alternating-field demagnetization results show that one main process remagnetized the rocks. These results support the hypothesis that intense and possibly localized post-impact hydrothermal alteration enhanced the magnetization of the clast-rich impact melt rocks by crystallization of magnetite within the center of the Haughton impact structure. Subsequent erosion was followed by in-situ concentration in the subsurface leading to large magnetic gradient on surface.