Myotis stalkeri is a cave roosting species that is assumed to primarily forages on fish due to its morphology, but it is likely that it also forages on insects on a regular basis as evidenced by (Aizpurua and Alberdi 2018), a trait that is common among fishing Myotis species. The species is assumed to forage over freshwater, and it is possible that it also forages above the sea. A species of Myotis was observed foraging above the seashore in Raja Ampat, but it is not known whether it was M. stalkeri or M. moluccarum (Bouillard N. pers. comm.).

This species is known to roost alongside other bat species (Flannery 1995, Meining 2002). Individuals found on the Kai Islands in 1993 were in a small colony, sharing the roost with five other bat species (Flannery 1995). The colony on Gebe consisted of about 100 individuals in a limestone cave, surrounded by tall forest (Flannery 1995). At the time of the collection, one of two adult females collected was carrying a single young bat. Further, a cave roost on Waigeo was located near the sea and surrounded by tropical forest. 
The generation length of Myotis stalkeri is estimated to be 5.8 (Pacifici et al. 2013).

This species has been recorded on four (4) islands in Indonesia with a total land area of less than 10,000 km². One of those islands is in the Malukus: Gebe (November 1991, Flannery 1995); two are in Raja Ampat: Waigeo and Batanta (2000 and 2005; Helgen 2007 and Meinig 2002); and the last one is in the Kai islands: Kai Kecil (1907 and 1993; Flannery 1995).

It has only been recorded below 250 m asl (Meinig 2002).

This species is not believed to be present in any protected areas and there are no known species-specific conservation initiatives in place for the species. Research is needed to document the species’ population size and trends, ecology, habitat requirements and the impact of the suspected threats.
Protection of known roosting sites and important foraging areas is needed.