Myotis nattereri forms maternity colonies in tree hollows, spaces beneath loose bark and in bat boxes, but also in crevices in buildings and bridges, and frequently in cattle stables as well as in hollow blocks. Nurseries number 30-80 individuals, but in buildings, they can include up to 200 females. It hibernates in underground habitats (caves, cellars and mines), usually solitary or in small clusters of 2-5 individuals (Simon et al. 2012), but > 300 bats hibernate in Nietoperek, Poland (EUROBATS 2019). The species is a foraging generalist that hunts by foliage gleaning and aerial hawking close to vegetation in many habitats such as meadows, pastures, orchards, broadleaved woods, open coniferous forests and riparian areas, which may be locally very important (reviewed in Kyheröinen et al. 2019). It also hunts inside sheds, where it detects copulating flies through passive listening and gleans them off the walls (Siemers et al. 2012).

Radiotracking studies have shown that bats show different foraging ranges in different landscapes, but generally cover distances of a few km from the roost. In Germany, average distances of 1.5 km were found (Simon et al. 2004), while in the UK, the bats mostly foraged within 3 km of the roost, and the longest recording distance was 5.8 km (Smith and Racey 2008). The diet of this species is broad but is dominated by diurnal dipterans in summer (reviewed in Kyheröinen et al. 2019), whereas winter prey comprises much non-volant arthropod prey, Aranea, Isopoda and lepidopteran larvae (Hope et al. 2014). Myotis nattereri is deemed to be sedentary, but it might be a facultative migrant, and the longest seasonal movement recorded was 157 km in Germany (Hutterer et al. 2005).

Myotis nattereri sensu stricto is part of the M. nattereri complex, characterized by highly diverged lineages. The following components of the complex occur in Europe: M. escalerai (Ibáñez et al. 2006), M. crypticus (Juste et al. 2019), and Myotis sp. C (Puechmaille et al. 2012), the latter not yet formally described and endemic to Corsica. The range of altitudes where M. nattereri can be found varies between 0 and 2,000 m asl. The AOO has not been estimated, but based on the available locality records, it is expected to exceed the threshold for a threatened category.

Myotis nattereri occurs across a broad European range: it is found north and east of the Alps, including the British Isles, Switzerland, France, Germany, Scandinavia, the Baltic states, the Balkans, the Carpathians and entire Eastern Europe up to the Urals in European Russia; it is considered to be endemic to the European region at present. However, the existence of hybrids in secondary contact zones between this species and the sibling Myotis crypticus as well as the lack of comprehensive molecular assessment across the entire range of the species makes the picture still unclear in certain regions.

Myotis nattereri is protected by national legislation in most of the main range states. There are also international legal obligations for its protection through the EUROBATS Agreement and the Bern Convention. It is listed under Annex IV of 92/43/EEC Habitats Directive. According to the 2013-2018 art. 17 reporting made within the framework of this Directive, the conservation status of this species in the EU is classified as unfavourable-inadequate in all Biogeographic Regions except the Continental and the Atlantic Regions, where it is favourable. However, the other cryptic species occurring in Europe are not assessed separately, so this evaluation has mixed data regarding all such species (for example, Iberian data were used, but in Iberia, only M. escalerai and M. crypticus occur).

The preservation of this species requires strict protection of its underground and overground roosting sites, as well as the general conservation of habitat quality in forest, riparian and agricultural foraging sites, maintaining forest unevenness, decaying trees, as well as reducing the use of pesticides and artificial illumination.