Impact-generated hydrothermal systems have been suggested as favourable environments for deep microbial ecosystems on Earth, and possibly beyond. Fossil evidence from a handful of impact craters worldwide have been used to support this notion. However, as always with mineralized remains of microorganisms in crystalline rock, certain time constraints with respect to the ecosystems and their subsequent fossilization are difficult to obtain. Here we re-evaluate previously described fungal fossils from the Lockne crater (458 Ma), Sweden. Based on in-situ Rb/Sr dating of secondary calcite-albite-feldspar (356.6 ± 6.7 Ma) we conclude that the fungal colonization took place at least 100 Myr after the impact event, thus long after the impact-induced hydrothermal activity ceased. We also present microscale stable isotope data of ¹³C-enriched calcite suggesting the presence of methanogens contemporary with the fungi. Thus, the Lockne fungi fossils are not, as previously thought, related to the impact event, but nevertheless have colonized fractures that may have been formed or were reactivated by the impact. Instead, the Lockne fossils show similar features as recent findings of ancient microbial remains elsewhere in the fractured Swedish Precambrian basement and may thus represent a more general feature in this scarcely explored habitat than previously known.