The mineralogy of comet 81P/Wild 2 particles, collected in aerogel by the Stardust mission, has been determined using synchrotron Fe‐K X‐ray absorption spectroscopy with in situ transmission XRD and X‐ray fluorescence, plus complementary microRaman analyses. Our investigation focuses on the terminal grains of eight Stardust tracks: C2112,4,170,0,0; C2045,2,176,0,0; C2045,3,177,0,0; C2045,4,178,0,0; C2065,4,187,0,0; C2098,4,188,0,0; C2119,4,189,0,0; and C2119,5,190,0,0. Three terminal grains have been identified as near pure magnetite Fe3O4. The presence of magnetite shows affinities between the Wild 2 mineral assemblage and carbonaceous chondrites, and probably resulted from hydrothermal alteration of the coexisting FeNi and ferromagnesian silicates in the cometary parent body. In order to further explore this hypothesis, powdered material from a CR2 meteorite (NWA 10256) was shot into the aerogel at 6.1 km s−1, using a light‐gas gun, and keystones were then prepared in the same way as the Stardust keystones. Using similar analysis techniques to the eight Stardust tracks, a CR2 magnetite terminal grain establishes the likelihood of preserving magnetite during capture in silica aerogel.